Patent Application
20210061881
This application is being filed electronically via EFS-Web and includes an electronically submitted sequence listing in .txt format. The .txt file contains a sequence listing entitled “AT-030_03US_SL.txt” created on Aug. 27, 2020, and having a size of 570,950 bytes. The sequence listing contained in this .txt file is part of the specification and is incorporated herein by reference in its entirety.
Adoptive transfer of immune cells (e.g. T-cells) genetically modified to recognize malignancy-associated antigens is showing promise as a new approach to treating cancer. For example, T-cells can be genetically modified to express chimeric antigen receptors (CARs), which are fusion proteins comprised of an antigen recognition moiety and T-cell activation domains.
T-cell proliferation, cytotoxic potency and persistence is driven by signal transduction pathways. Conventional CAR designs provide two signals—CD3zeta activation (Signal 1) and co-stimulation (Signal 2, e.g. via 4-1BB, OX40, and/or CD28 expression). In some contexts, a third signal (Signal 3), cytokine-induced cytokine receptor signaling (e.g. cytokine support for immune potentiation), may be desirable. Approaches to provide Signal 3 have however been met with significant limitations.
One approach to provide cytokine support includes combining CAR-T-cell therapy with systemic infusions of recombinant cytokines/cytokine mimetics, and engineering CAR-T-cells to secrete/express cytokines extracellularly. As cytokines have pleiotropic effects and can also impact the function of other cell types, the systemic administration or production of immune-potentiating cytokines by CAR-T-cells have at least two major drawbacks: (i) these approaches can cause systemic toxicity in humans, and (ii) in the context of allogeneic CAR-T-cell therapy, these approaches may cause bystander host immune-activation that could accelerate the rejection of allogeneic CAR-T-cells, thereby compromising therapeutic efficacy. Another approach to provide cytokine support was based on introducing a constitutively activated dimerized cytokine receptor, an IL-7Ra—this limits the nature (IL-7 signaling only) and magnitude of signaling output. Yet another approach to provide cytokine support involved incorporating Signal 3 directly into the CAR molecule (Nat Med. 2018 March; 24(3):352-359.). A limitation of this approach is that the strength of Signal 3 is dependent on the strength of CAR activation. In the absence of target (and CAR activation), Signal 3 would not be transduced.
Needed are solutions to circumvent these drawbacks by targeting cytokine signals specifically to CAR-T-cells in a context-dependent manner, thus allowing for an improved safety profile and therapeutic efficacy. Provided herein and compositions and methods that address this need.
Provided herein are chimeric cytokine receptors comprising TGF-β binding domains. Provided herein are inducible TGF-β-driven chimeric cytokine receptors, active when engaged with a ligand of the transforming growth factor beta cytokine family (TGF-β ligands, e.g., TGF-β1, TGF-β2, and TGF-β3) or activation with an anti-TGF-β-receptor antibody. When present on chimeric antigen receptor (CAR)-bearing immune cells, and engaged with TGF-β ligands and/or activation with an anti-TGF-βR antibody, such receptors allow for increased cytokine receptor signaling (Signal 3), leading to increased immune cell activation, proliferation, persistence, and/or potency of the CAR-bearing immune cells. Accordingly, the chimeric cytokine receptors of the disclosure allow for cytokine signals to be transmitted into the immune cell with endogenous TGF-β ligands, whereby blocking their immune-suppressive signals, and converting them into immune-potentiating signals that can work in concert with, or synergize, CAR-driven activity. Moreover, as clinically approved anti-TGF-β receptor antibodies can cluster and activate the chimeric cytokine receptors of the disclosures, patients treated with anti-TGF-β receptor may benefit not only from the blockage of the endogenous TGF-β signaling, but from also the activation of cytokine signaling in cells bearing the chimeric cytokine receptors. Also provided herein are constitutively active TGF-β-driven of TGF-β binding domain-containing chimeric cytokine receptors; such receptors continue to signal in the absence of an inducer, but can be further induced or can exhibit further improved properties or activities, for example, in the presence of a TGF-β ligand or an anti-TGF-βR antibody. In some embodiments, the TGF-βR is TGF-βR2, and the antibody is an anti-TGF-βR2 antibody. As used herein, “TGF-beta” is used interchangeably with “TGF-β.”
Accordingly, in one aspect, provided herein is a chimeric cytokine receptor comprising: (a) a binding domain comprising an extracellular portion of a TGF-β receptor, or a TGF-β antigen binding domain; (b) a transmembrane domain; (c) a Janus Kinase (JAK)-binding domain; and (d) a recruiting domain. As used herein, “extracellular portion” refers to any portion of an extracellular domain of a TGF-β receptor.
In a related aspect provided herein is a polynucleotide encoding any one of the chimeric cytokine receptors of the disclosure, and an expression vector comprising such a polynucleotide. In some embodiments, the polynucleotide further encodes for a chimeric antigen receptor (CAR), wherein the CAR binds to a target of interest. The target of interest can be any molecule of interest, including, for example, without limitation any one or more of those presented in Table 8.
In a further aspect, provided herein is an engineered immune cell comprising at least one chimeric cytokine receptor of the disclosure. In another aspect, provided herein is an engineered immune cell comprising at least one chimeric antigen receptor (CAR) and at least one chimeric cytokine receptor of the disclosure. In some embodiments the immune cell is a T-cell. In some embodiments the immune cell is an allogeneic immune cell. In other embodiments, the immune cell is an autologous immune cell. The immune cell may be selected from the group consisting of: T-cell, dendritic cell, killer dendritic cell, mast cell, NK-cell, macrophage, monocyte, B-cell and an immune cell derived from a stem cell. In a related aspect, provided herein is a pharmaceutical composition comprising any of the engineered immune cells of the disclosure, and a kit comprising such a pharmaceutical composition. Also provided herein is a method of making the immune cell.
In another aspect, provided herein is a method of treating a cancer in a subject, comprising administering to the subject a therapeutically effective amount of any of the engineered immune cells described herein.
Provided herein are chimeric cytokine receptors comprising TGF-β binding domains. Provided herein are inducible chimeric cytokine receptors, active when engaged with TGF-β ligands (e.g. TGF-β1, TGF-β2, and/or TGF-β3) or activation with an anti-TGF-β-receptor antibody. Also provided herein are constitutively active chimeric cytokine receptors comprising TGF-β binding domains. Also provided herein are chimeric antigen receptor (CAR)-bearing immune cells (CAR-I-cells, e.g. CAR-T-cells), expressing the chimeric cytokine receptors of the disclosure. In some embodiments, the constitutively active chimeric cytokine receptors exhibit improved properties or activities when engaged with a TGF-β ligand or activation with an anti-TGF-β-receptor antibody, as compared with constitutively active chimeric cytokine receptors without a TGF-β binding domain. Also provided herein are methods of making and using the chimeric cytokine receptors.
The chimeric cytokine receptors of the disclosure activate signaling upon binding of a TGF-β ligand (for example, TGF-β1, TGF-β2, and/or TGF-β3), or an anti-TGF-β-receptor antibody. These receptors activate signaling when monomers of the receptor cluster and/or dimerize. The chimeric cytokine receptors of the disclosure are dual-function chimeric cytokine receptors which can simultaneously neutralize the immune-suppressive effects of a TGF-β ligand, and mimic the transmission of an immune-potentiating cytokine signal.
In some embodiments, a monomer of the chimeric cytokine receptor of the disclosure comprises: (a) a binding domain capable of binding a TGF-β ligand or an anti-TGF-β-receptor antibody; (b) a transmembrane domain; (c) a Janus Kinase (JAK)-binding domain; and; (d) a STAT-recruiting domain (e.g. from the cytoplasmic domain of a receptor; e.g. from a cytokine receptor). Each domain can be linked either directly or via one or more peptide linkers. In some embodiments, a monomer of the chimeric cytokine receptor of the disclosure comprises: (a) a binding domain capable of binding a TGF-β ligand or an anti-TGF-β-receptor antibody; (b) a transmembrane domain; (c) a Janus Kinase (JAK)-binding domain; and; (d) a recruiting domain (e.g. from the cytoplasmic domain of a receptor; e.g. from a cytokine receptor). The recruiting domain can be a STAT-recruiting domain, an AP1—recruiting domain, a Myc/Max recruiting domain; or a NFkB-recruiting domain. In some embodiments, the chimeric cytokine receptors are clustered and activated when they bind to TGF-β ligands, and/or are clustered and activated with an anti-TGF-β-receptor antibody. The chimeric cytokine receptors activate signaling upon for example binding a TGF-β ligand, and/or a TGF-β-receptor antibody. In some embodiments, the TGF-β receptor antibody is, without limitation, PF-03446962 or LY3022859. In some embodiments, the chimeric cytokine receptors are constitutively clustered or dimerized.
As used herein, “TGF-β ligand,” refers to TGF-β1, TGF-β2, and TGF-β3, and isoforms and derivatives thereof. It should be understood that “TGF-β ligand” and “TGF-β” are used interchangeably herein.
A. Binding Domains
The chimeric cytokine receptors of the disclosure comprise a binding domain capable of binding a TGF-β ligand or an anti-TGF-β-receptor antibody. As referred to herein, a binding domain is the domain of the chimeric cytokine receptor that extends into the extracellular space. The binding domain binds and sequesters TGF-β away from the endogenous TGF-β receptor, thereby preventing or reducing TGF-β-induced immune-suppression. The binding domains of the disclosure bind with TGF-β ligands and anti-TGF-β-receptor antibodies, leading to binding-induced signal transduction.
In some embodiments, the binding domain comprises an extracellular portion of a TGF-β receptor, for example the extracellular portion of TGFβR1 or TGFβR2.
In some embodiments, the binding domain comprises an extracellular portion of a wild type TGFβ receptor. In some embodiments, the TGF-β receptor comprises one or more mutations that enhance or alter the affinity to the binding to the TGFβ ligands.
In some embodiments, the binding domain comprises the extracellular portion of a wild type TGFβR1 or TGFβR2; in some embodiments, the binding domain comprises the extracellular portion of a wild type TGFβR1 or TGFβR2 and comprises the amino acid sequence of SEQ ID NOS: 2 or 3, respectively.
In some embodiments, the binding domain comprises mutations to the extracellular portion of a wild type TGF-β receptor. In some embodiments, the binding domain comprises mutations to the extracellular portion of a wild type TGF-β receptor, and comprises the amino acid sequences of any one of SEQ ID NO: 4 to SEQ ID NO: 20. In some embodiments, the chimeric cytokine receptor comprises a binding domain that is at least 80%, 85%, 90%, 95%, 98%, or 99%, or 100% identical to any one of the amino acid sequences of SEQ ID NOs: 4-20. In some embodiments, the binding domain does not comprise a signal sequence.
Table 1 shows exemplary binding domain amino acid sequences of the disclosure. It is noted that the expression and extracellular location of the exemplary binding domain sequences, such as TGF-β receptor amino acid sequences, can be achieved with the use of a signal sequence. In an exemplary embodiment, a CD8 signal sequence (CD8SS) MALPVTALLLPLALLLHAARP (SEQ ID NO: 1) is utilized. In some embodiments, the binding domain comprises the extracellular domain of wild type TGFβR2 comprising the amino acid sequence of SEQ ID NO:159. In some embodiments, the signal sequence is the endogenous signal sequence of human TGF-βR2.
MGRGLLRGLWPLHIVLWTRIASTIPPHVQKSVNN
In some embodiments, the chimeric cytokine receptor is a dominant negative (DN) wherein the binding domain of the TGF-β receptor is expressed, but the chimeric cytokine receptor does not comprise an intracellular signaling domain—the chimeric cytokine receptor can bind TGF-β but does not transmit a positive signal (DN chimeric cytokine receptor). In some embodiments, the TGF-β receptor is TGFβR1 (dominant-negative TGFβR1, or TGFβR1 DN) and comprises the amino acid sequence of SEQ ID NO: 2. In some embodiments, the TGF-β receptor is TGFβR2 (dominant-negative TGFβR2, or TGFβR2 DN) and comprises the amino acid sequence of SEQ ID NO: 3. TGF-β receptor dominant negative sequences may be expressed with the aid of a signal sequence, e.g. a CD8SS signal sequence of SEQ ID NO: 1. Example schematics of a DN chimeric cytokine receptor are shown in
In other embodiments, the binding domain comprises a TGF-β antigen binding domain. Such antigen binding domains include, but are not limited to, a single chain variable fragment (scFv) that can bind the TGF-β ligands, and single domain antibodies (nanobodies). These scFvs and single domain antibodies may include commercially available scFvs and single domain antibodies, and those derived from, for example, camelid and shark antibodies.
In other embodiments, the binding domain comprises a TGF-β antigen binding domain, wherein the antigen binding domain comprises a Fab fragment.
B. Transmembrane Domains
The chimeric cytokine receptors of the disclosure comprise transmembrane domains. Such transmembrane domains are coupled to the extracellular binding domain on the N-terminus, and to additional intracellular/cytoplasmic domains on the C-terminus. In some embodiments, the coupling is achieved optionally through a linker.
As used herein, the transmembrane domains are capable of insertion into the membrane of a cell in which it is expressed. In some embodiments, the transmembrane domains of the disclosure span a cellular membrane, and comprise an extracellular portion, and/or an intracellular portion.
In some embodiments, the transmembrane domains of the disclosure are engineered and do not resemble any naturally occurring transmembrane domain, e.g. they are non-naturally occurring.
In other embodiments, the transmembrane domains of the disclosure are derived from naturally occurring receptors.
In some embodiments, the transmembrane and/or JAK domains of the disclosure are derived from, for example, one or more of the following receptors: erythropoietin receptor (EpoR), Interleukin 6 signal transducer (GP130 or IL6ST), prolactin receptor (PrlR), growth hormone receptor (GHR), granulocyte colony-stimulating factor receptor (GCSFR), and thrombopoietin receptor/myeloproliferative leukemia protein receptor (TPOR/MPLR). When derived from naturally occurring receptors, the entire receptor, or the entire transmembrane sequence of the receptor may not be necessary to effectuate constitutive activation and constitutive JAK binding/activation on the intracellular portion. Accordingly fragments of naturally occurring receptors may be utilized. Furthermore, certain mutations may be introduced into the transmembrane domains derived from naturally occurring receptors, to further tune the downstream JAK-dependent signaling. In some embodiments, the chimeric cytokine receptor of the disclosure comprises a portion or a fragment of a naturally occurring receptor, e.g., the transmembrane and/or JAK binding/activation domain of the naturally occurring receptor, optionally comprising one or more mutations therein (e.g., one or more deletions, insertions and/or substitutions).
In some embodiments, the transmembrane and/or JAK domains of the disclosure is derived from the naturally occurring EpoR receptor.
In some embodiments, the transmembrane and/or JAK domains of the disclosure is derived from the naturally occurring GP130 receptor.
In some embodiments, the transmembrane and/or JAK domains of the disclosure is derived from the naturally occurring PrlR receptor.
In some embodiments, the transmembrane and/or JAK domains of the disclosure is derived from the naturally occurring GHR receptor.
In some embodiments, the transmembrane and/or JAK domains of the disclosure is derived from the naturally occurring GCSF receptor.
In some embodiments, the transmembrane and/or JAK domains of the disclosure is derived from the naturally occurring TPOR receptor. When the TPOR transmembrane domain assumes a permissive homodimeric conformation, such as in response to a ligand or forced activation resulting from the introduction of engineered modifications, it is capable of activating downstream cytokine signaling in a JAK2-dependent fashion. The introduction of various modifications to the TPOR transmembrane domain can result in the following: the immune-potentiating cytokine signal may either be (a) quiescent until induced to activate in the presence of extracellular TGF-β, or (b) constitutively active regardless of TGF-β availability.
Table 2 provides exemplary full length sequences of naturally occurring receptors provided in the disclosure, from which the transmembrane and/or JAK domains are derived.
sapiens]
In some embodiments, the transmembrane domain of the disclosure is derived from a truncated, or otherwise modified version of the naturally occurring TPOR/MPLR receptor shown in Table 2.
Table 3 shows exemplary transmembrane amino acid sequences, coupled to intracellular JAK2 binding domain sequences.
In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 27. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 28. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 29. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 30. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 31. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 32. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 33. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 34. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 35. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 36. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 37. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 38. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 39. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 40. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 41. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 42. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 43. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 44. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 45. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 46. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 47. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 48. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 49. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 50. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 51. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 52. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 53. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 54. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 55. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 56. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 57. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 58. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 59. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 60. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 61. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 62. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 63. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 64. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 65. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 66. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 67. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 68. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 69. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 70. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 71. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 72. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 73. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 74. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 75. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 76. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 77. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 78. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 79. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 160. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 217. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises the amino acid sequence of SEQ ID NO: 218, SEQ ID NO: 219, SEQ ID NO: 220, SEQ ID NO: 221, SEQ ID NO: 222, SEQ ID NO: 223, SEQ ID NO: 224, SEQ ID NO: 225, SEQ ID NO: 226, SEQ ID NO: 227, SEQ ID NO: 228, SEQ ID NO: 229, SEQ ID NO: 230, SEQ ID NO: 231, SEQ ID NO: 232, SEQ ID NO: 233, or SEQ ID NO: 234. In some embodiments, the transmembrane domain of the chimeric cytokine receptor comprises an amino acid sequence that is at least 80%, 85%, 90%, 95%, 98%, or 99%, or 100% identical to the amino acid sequence of any one of SEQ ID NOs: 27-79, 160, and 217-234.
In some embodiments, the chimeric cytokine receptor (CCR) comprises the binding domain comprising the amino acid sequence of SEQ ID NO: 3, 4 or 159, and the transmembrane and JAK2 binding domain comprising the amino acid sequence of SEQ ID NO: 64, 69, or 70. In some embodiments, the CCR is inducible. In some embodiments, the CCR comprises the binding domain comprising the amino acid sequence of SEQ ID NO: 3, 4 or 159, and the transmembrane and JAK2 binding domain comprising the amino acid sequence of SEQ ID NO: 38, 39, 40 or 53. In some embodiments, the CCR comprises the binding domain comprising the amino acid sequence of SEQ ID NO: 3, 4 or 159, and the transmembrane and JAK2 binding domain comprising the amino acid sequence of SEQ ID NO: 59, 60, 160, or 217. In some embodiments, the CCR is constitutively active. In some embodiments, the constitutively active CCR of the disclosure dimerizes without a TGF-β ligand.
C. Janus Kinase (JAK)-Binding Domains
The chimeric cytokine receptors of the disclosure comprise intracellular JAK-binding domains. The JAK-binding domain is coupled to the C-terminus of the transmembrane domain, either directly, or via a linker. The JAK-binding domain is coupled to the transmembrane domain on the intracellular side of the chimeric cytokine receptor.
In some embodiments, the JAK-binding domain is a JAK-1-binding domain, a JAK-2 binding domain, a JAK-3 binding domain, or a TYK2 binding domain.
In some embodiments, the JAK-binding domains of the chimeric cytokine receptors of the disclosure are naturally occurring, and derived from a naturally occurring receptor.
In some embodiments, the JAK-binding domains of the chimeric cytokine receptors of the disclosure are synthetic.
In some embodiments, the chimeric cytokine receptor comprises a transmembrane and JAK2 binding domain that is at least 80%, 85%, 90%, 95%, 98% or 99%, or 100% identical to any one of the amino acid sequences of SEQ ID NOs: 27-79, 160 and 217-234.
Table 3 provides exemplary amino acid sequences for the transmembrane and JAK2 binding domains of the disclosure. In some embodiments, the transmembrane and JAK2 binding domain comprises one or more mutations, e.g., one or more deletions, insertions and/or substitutions of the wild type sequences. In some embodiments, the transmembrane and JAK2 binding domain comprises one or more substitutions at amino acid positions H499, S505 and W515 of the wild type TPOR/MPLR sequence. See Table 3. In some embodiments, the transmembrane and JAK2 binding domain comprises one or more substitutions at the amino acid positions K533 and K573 of the wild type TPOR/MPLR sequence. In some embodiments, the transmembrane and JAK2 binding domain, e.g., as shown in Table 3, may be combined with a TGFβR2 ectodomain as disclosed herein, e.g., in Table 1, or a PD-1 ectodomain (such as a high affinity PD-1 ectodomain, as indicated in SEQ ID NO: 274 or 275 in Table 6) and a recruiting domain to form a chimeric cytokine receptor. In some embodiments, the transmembrane and JAK2 binding domain may be combined with a recruiting domain to form a chimeric cytokine receptor without an ectodomain, see e.g., SEQ ID NOs: 272 or 273. See also U.S. Ser. No. 16/804,917, filed on Feb. 28, 2020, and U.S. Ser. No. 16/804,545, filed on Feb. 28, 2020, both of which are incorporated herein by reference in their entireties.
D. Recruiting Domains
The chimeric cytokine receptors of the disclosure comprise cytoplasmic domains comprising recruiting domains (which may also be referred to as “signaling domains”). The recruiting domain can be a STAT-recruiting domain, an AP1—recruiting domain, a Myc/Max recruiting domain; or an NFkB-recruiting domain. In some embodiments, the recruiting domain is a Signal Transducer and Activator of Transcription (STAT)—recruiting (Stat-activating) domains from receptor tails (cytotails) or from cytokine receptor tails. These intracellular recruiting domains of the chimeric cytokine receptors of the disclosure allow for the propagation of Signal 3 in an immune cell comprising a CAR and a chimeric cytokine receptor (e.g. a CAR-T-cell with a chimeric cytokine receptor of the disclosure). Cytokine signaling propagated through the Stat-recruiting domain allows for the cytokine-based immune potentiation of the cell. In some embodiments, the immune-potentiation is homeostatic, e.g. signaling gives rise to increase in immune cells bearing the CAR. In some embodiments, the immune-potentiation is inflammatory, e.g. signaling gives rise to increase in the potency of the immune cells bearing the CAR. In some embodiments, the immune-potentiation prevents exhaustion, e.g. signaling maintains the long-term functionality of immune cells bearing the CAR.
In some embodiments, the recruiting domains of the disclosure are synthetic, and do not resemble any naturally occurring receptor fragment.
In some embodiments, the Stat-recruiting domains of the disclosure are synthetic, and do not resemble any naturally occurring receptor fragment.
In other embodiments, the Stat-recruiting domains of the disclosure are derived from cytoplasmic tails of naturally occurring receptors, e.g. derived from naturally occurring cytokine receptors. In some embodiments, the chimeric cytokine receptor comprises a portion or a fragment of a naturally occurring receptor, e.g., the intracellular Stat-recruiting domain of the naturally occurring receptor, optionally with one or more mutations therein (e.g., one or more deletions, insertions and/or substitutions). These cytoplasmic tails of naturally occurring receptors may be the regions downstream of the JAK-activating domains of the transmembrane domain of the receptor. The Stat-recruiting domains of the chimeric cytokine receptors comprise at least one STAT-recruiting domain from at least one receptor. In some embodiments, the Stat-recruiting domain comprises at least one STAT1-recruiting domain. In some embodiments, the Stat-recruiting domain comprises at least one STAT2-recruiting domain. In some embodiments, the Stat-recruiting domain comprises at least one STAT3-recruiting domain. In some embodiments, the Stat-recruiting domain comprises at least one STAT4-recruiting domain. In some embodiments, the Stat-recruiting domain comprises at least one STAT5-recruiting domain. In some embodiments, the STAT-recruiting domain comprises at least one STAT6-recruiting domain. In some embodiments, the Stat-recruiting domain comprises at least one STAT7-recruiting domain.
In some embodiments, the naturally occurring receptor from which the STAT-recruiting domain is derived, is a not a cytokine receptor.
In some embodiments, the naturally occurring receptor from which the Stat-recruiting domain is derived, is a cytokine receptor. Exemplary cytokine receptors through which T-cell-immune potentiating cytokines signal include, but are not limited to IL-2 receptor, IL-7 receptor, IL-15 receptor, IL12 receptor, and IL-21 receptor. In some embodiments, the cytokine receptor from which the STAT-recruiting domain is derived contains phosphorylatable tyrosine residues downstream of the cognate JAK-binding motifs, and one or more signaling domains of interest may be fused downstream of the transmembrane domain to generate single or multiple signaling outputs. In alternative embodiments, the receptor from which the Stat-recruiting domain is derived, is not a cytokine receptor. By choosing the Stat-recruiting domain of the chimeric cytokine receptor, the receptor can be redirected to signaling of choice. In some embodiments, the chimeric cytokine receptor comprises two or more Stat-recruiting domains from more than one receptor. In some embodiments, the two or more Stat-recruiting domains are linked with or without a peptide linker.
Table 4 provides exemplary receptors from which Stat-recruiting domains (signaling domains) of the chimeric cytokine receptors of the disclosure are derived. Table 5a provides exemplary amino acid sequences of recruiting domains of the disclosure.
In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 80. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 81. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 82. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 83. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 84. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 85. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 86. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 87. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 88. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 89. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 90. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 91. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 92. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 93. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 94. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 95. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 96. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 97. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 98. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 99. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 100. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 101. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 102. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 103. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 104. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 105. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 106. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 107. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 108. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 109. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 110. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 111. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 112. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 113. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 114. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 115. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 116. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 117. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 118. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 119. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 120. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 121. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 122. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of the STAT-recruiting domain of SEQ ID NO: 161. In some embodiments, the chimeric cytokine receptor comprises a recruiting domain that comprises an amino acid sequence that is at least 80%, 85%, 90%, 95%, 98%, or 99%, or 100% identical to any one of the amino acid sequences of SEQ ID NOs: 80-122 and SEQ ID NO: 161.
In some embodiments, the Stat-recruiting domain of a chimeric cytokine receptor of the disclosure comprises a STAT-recruiting domain from one receptor.
In order to generate multiple outputs, one or more STAT-recruiting domains may be joined in tandem to mimic signaling from one or more cytokines.
In some embodiments, the STAT-recruiting domain comprises portions of more than one receptor, e.g. comprising more than one STAT-recruiting domain. In such embodiments, a tandem cytokine signaling domain is provided, allowing for enhanced signaling. Accordingly, in some embodiments, the STAT-recruiting domain of a monomer of the chimeric cytokine receptor of the disclosure comprises the STAT-recruiting domains from more than one receptor, e.g. comprises the STAT-recruiting domains from two, three, four, five, or even six receptors. For example, in some embodiments, STAT-recruiting domains can be linked in tandem to stimulate multiple pathways (e.g., the IL7R(316-459)-IL12Rb2(775-825) fragment fusion for pro-persistence STAT5 and pro-inflammatory STAT4; IL7R(316-459)-IL2Rbsmall(393-433,518-551) for pro-persistence; IL7R(316-459)-EGFR(1122-1165) for pro-persistence and anti-exhaustion; IL2Rbsmall(393-433,518-551)-EGFR(1122-1165) for pro-persistence and anti-exhaustion).
When generating multiple outputs, the proximity of individual STAT-recruiting domains to the cell membrane can influence the strength of their respective signaling outputs. Table 5b shows examples of chimeric cytokine receptors with the dual outputs, where each output can be placed either proximal or distal to the cell membrane.
Without being bound to theory or mechanism, in some embodiments, a JAK-protein (JAK1, JAK2, JAK3, or TYK2) is bound to a chimeric cytokine receptor of the disclosure (comprising a binding domain, a transmembrane domain, a JAK-binding domain, and a recruiting domain). In some embodiments, in the presence of (e.g. binding to) a TGF-β ligand or an anti-TGF-β-receptor antibody, the chimeric cytokine receptor clusters and allows for the two bound JAK-proteins to become activated, which in turn phosphorylate tyrosine residues on the recruiting domain of the chimeric receptor. The phosphorylated recruiting domains are then capable of binding the recruited proteins (e.g. a phosphorylated STAT-recruiting domain binds a STAT-protein), which in turn effectuate transcription events in the nucleus.
E. Exemplary TGF-β-Driven Chimeric Cytokine Receptors
Context-dependent chimeric cytokine receptors of the disclosure may be expressed with a signal sequence, e.g. a CD8SS of SEQ ID NO: 1. Table 6 shows exemplary context-dependent cytokine receptor sequences of the disclosure. The receptors may be expressed with a signal sequence, e.g. a CD8SS of SEQ ID NO: 1.
In some embodiments, the chimeric cytokine receptor of the disclosure comprises a TGF-β binding domain comprising an amino acid sequence of any one of SEQ ID NOs: 3-20, and 159, a transmembrane and JAK2 binding domain comprising an amino acid sequence of any one of SEQ ID NOs: 27-79, 160 and 217-234, and a recruiting domain comprising an amino acid sequences of any one of SEQ ID NOs: 80-122 and 161. In some embodiments, the chimeric cytokine receptor does not comprise a signal sequence.
In some embodiments, the chimeric cytokine receptor of the disclosure comprises a TGF-β binding domain comprising the amino acid sequence selected from the group consisting of SEQ ID NOs: 3, 4, and 159, a TPOR/MPLR transmembrane and JAK2 binding domain comprising the amino acid sequence selected from the group consisting of SEQ ID NOs: 38, 39, 40, 53, 59, 60, 61, 64, 69, 70, 160 and 217-234, and a recruiting domain comprising the amino acid sequence selected from the group consisting of SEQ ID NOs: 80, 99, 111, 112, and 161. Optionally, the chimeric cytokine receptor comprises a signal sequence that comprises for example the amino acid sequence of SEQ ID NO:1.
In some embodiments, the chimeric cytokine receptor comprises a binding domain comprising the amino acid sequence of SEQ ID NO: 3, 4 or 159, a transmembrane and JAK2 binding domain comprising the amino acid sequence of SEQ ID NO: 64, 69, or 70, and a recruiting domain comprising the amino acid sequence of SEQ ID NO: 80, 99, 111, 112, or 161. In some embodiments, the chimeric cytokine receptor is inducible. In some embodiments, the chimeric cytokine receptor comprises a binding domain comprising the amino acid sequence of SEQ ID NO: 3, 4 or 159, a transmembrane and JAK2 binding domain comprising the amino acid sequence of SEQ ID NO: 38, 39, 40 or 53, and a recruiting domain comprising the amino acid sequence of SEQ ID NO: 80, 99, 111, 112, or 161. In some embodiments, the chimeric cytokine receptor comprises a binding domain comprising the amino acid sequence of SEQ ID NO: 3, 4 or 159, a transmembrane and JAK2 binding domain comprising the amino acid sequence of SEQ ID NO: 59, 60, 160, or 217, and a recruiting domain comprising the amino acid sequence of SEQ ID NO: 80, 99, 111, 112, or 161. In some embodiments, the chimeric cytokine receptor is constitutively active. In some embodiments, the constitutively active chimeric cytokine receptor of the disclosure dimerizes without binding to a TGFβ ligand or an anti-TGFβR antibody. In some embodiments, the chimeric cytokine receptor of the disclosure inhibits TGFβR-mediated signaling and/or activates STAT-mediated signaling, either constitutively or induced by TGF-β, or an anti-TGFβR antibody. In some embodiments, the chimeric cytokine receptor is constitutively active and/or exhibits further enhanced activities or properties in the presence of a TGF-βR ligand, e.g., TGF-β, or an anti-TGF-βR antibody. In some embodiments, the TGF-βR is TGF-βR2, and the antibody is an anti-TGF-βR2 antibody.
In some embodiments, the chimeric cytokine receptor does not comprise a signal sequence. In some embodiments, the chimeric cytokine receptor comprises the TGFβR2 endogenous signal sequence or a signal sequence that comprise, e.g., the amino acid sequence of SEQ ID NO:1.
In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO: 123. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO: 124. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO: 125. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO: 126. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO: 127. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO: 128. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO: 129. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO: 130. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO: 131. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO: 132. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO: 133. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO: 134. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO: 135. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO: 136. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO: 137. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO: 138. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO: 139. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO: 140. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO: 141. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO: 142. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO: 143. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO: 144. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO: 145. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO: 146. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO: 147. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO: 148. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO: 149. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO: 150. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO: 151. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO: 162. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO: 163. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO: 164. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:165. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:166. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:167. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:168. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:169. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:170. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:171. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:172. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:173. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:174. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:175. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:176. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:177. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:178. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:179. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:180. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:181. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:182. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:183. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:184. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:185. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:186. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:187. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:188. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:189. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:190. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:191. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:192. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:193. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:194. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:195. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:196. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:197. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:198. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:199. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:200. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:201. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:202. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:203. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:204. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:205. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:206. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:207. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:208. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:209. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:210. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:211. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:212. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:213. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:214. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:215. In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:216.
In some embodiments, the chimeric cytokine receptor (CCR) comprises a binding domain comprising the amino acid sequence of SEQ ID NO: 159, a transmembrane and JAK2 binding domain comprising the amino acid sequence of SEQ ID NO: 40, and a recruiting domain comprising the amino acid sequence of SEQ ID NO: 80, 99, 111, 112, or 161. In some embodiments, the CCR comprises a binding domain comprising the amino acid sequence of SEQ ID NO: 159, a transmembrane and JAK2 binding domain comprising the amino acid sequence of SEQ ID NO: 53, and a recruiting domain comprising the amino acid sequence of SEQ ID NO: 80, 99, 111, 112, or 161. In some embodiments, the CCR comprises a binding domain comprising the amino acid sequence of SEQ ID NO: 4, a transmembrane and JAK2 binding domain comprising the amino acid sequence of SEQ ID NO: 38, and a recruiting domain comprising the amino acid sequence of SEQ ID NO: 80, 99, 111, 112, or 161. In some embodiments, the CCR comprises a binding domain comprising the amino acid sequence of SEQ ID NO: 4, a transmembrane and JAK2 binding domain comprising the amino acid sequence of SEQ ID NO: 39, and a recruiting domain comprising the amino acid sequence of SEQ ID NO: 80, 99, 111, 112, or 161. In some embodiments, the CCR comprises a binding domain comprising the amino acid sequence of SEQ ID NO: 4, a transmembrane and JAK2 binding domain comprising the amino acid sequence of SEQ ID NO: 40, and a recruiting domain comprising the amino acid sequence of SEQ ID NO: 80, 99, 111, 112, or 161. In some embodiments, the CCR comprises a binding domain comprising the amino acid sequence of SEQ ID NO: 4, a transmembrane and JAK2 binding domain comprising the amino acid sequence of SEQ ID NO: 53, and a recruiting domain comprising the amino acid sequence of SEQ ID NO: 80, 99, 111, 112, or 161. In some embodiments, the CCR comprises a binding domain comprising the amino acid sequence of SEQ ID NO: 159, a transmembrane and JAK2 binding domain comprising the amino acid sequence of SEQ ID NO: 70, and a recruiting domain comprising the amino acid sequence of SEQ ID NO: 80, 99, 111, 112, or 161. In some embodiments, the CCR comprises a binding domain comprising the amino acid sequence of SEQ ID NO: 159, a transmembrane and JAK2 binding domain comprising the amino acid sequence of SEQ ID NO: 69, and a recruiting domain comprising the amino acid sequence of SEQ ID NO: 80, 99, 111, 112, or 161. In some embodiments, the CCR comprises a binding domain comprising the amino acid sequence of SEQ ID NO: 4, a transmembrane and JAK2 binding domain comprising the amino acid sequence of SEQ ID NO: 64, and a recruiting domain comprising the amino acid sequence of SEQ ID NO: 80, 99, 111, 112, or 161. In some embodiments, the CCR comprises a binding domain comprising the amino acid sequence of SEQ ID NO: 4, a transmembrane and JAK2 binding domain comprising the amino acid sequence of SEQ ID NO: 69, and a recruiting domain comprising the amino acid sequence of SEQ ID NO: 80, 99, 111, 112, or 161. In some embodiments, the CCR comprises a binding domain comprising the amino acid sequence of SEQ ID NO: 4, a transmembrane and JAK2 binding domain comprising the amino acid sequence of SEQ ID NO: 70, and a recruiting domain comprising the amino acid sequence of SEQ ID NO: 80, 99, 111, 112, or 161. In some embodiments, the CCR comprises a binding domain comprising the amino acid sequence of SEQ ID NO: 159, a transmembrane and JAK2 binding domain comprising the amino acid sequence of SEQ ID NO: 160 or 219, and a recruiting domain comprising the amino acid sequence of SEQ ID NO: 80, 99, 111, 112, or 161. In some embodiments, the CCR comprises a binding domain comprising the amino acid sequence of SEQ ID NO: 159, a transmembrane and JAK2 binding domain comprising the amino acid sequence of SEQ ID NO: 223, 224, and a recruiting domain comprising the amino acid sequence of SEQ ID NO: 80, 99, 111, 112, or 161. In some embodiments, the CCR comprises a binding domain comprising the amino acid sequence of SEQ ID NO: 159, a transmembrane and JAK2 binding domain comprising the amino acid sequence of SEQ ID NO: 225 or 226, and a recruiting domain comprising the amino acid sequence of SEQ ID NO: 80, 99, 111, 112, or 161. In some embodiments, the CCR comprises a binding domain comprising the amino acid sequence of SEQ ID NO: 4, a transmembrane and JAK2 binding domain comprising the amino acid sequence of SEQ ID NO: 60 or 160, and a recruiting domain comprising the amino acid sequence of SEQ ID NO: 80, 99, 111, 112, or 161. In some embodiments, the CCR comprises a binding domain comprising the amino acid sequence of SEQ ID NO: 4, a transmembrane and JAK2 binding domain comprising the amino acid sequence of SEQ ID NO: 223, 224, and a recruiting domain comprising the amino acid sequence of SEQ ID NO: 80, 99, 111, 112, or 161. In some embodiments, the CCR comprises a binding domain comprising the amino acid sequence of SEQ ID NO: 4, a transmembrane and JAK2 binding domain comprising the amino acid sequence of SEQ ID NO: 225 or 226, and a recruiting domain comprising the amino acid sequence of SEQ ID NO: 80, 99, 111, 112, or 161
In some embodiments, the chimeric cytokine receptor of the disclosure comprises the amino acid sequence of SEQ ID NO:272, SEQ ID NO:273, SEQ ID NO:274, or SEQ ID NO:275. In some embodiments, the chimeric cytokine receptor comprises an amino acid sequence that is at least 80%, 85%, 90%, 95%, 98%, or 99%, or 100% identical to any one of the amino acid sequences of SEQ ID NOs: 123-216 and SEQ ID NOs: 272-275.
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MALPVTALLLPLALLLHAARPMGRGLLRGLWPLHIVLWTRIASTIP
MALPVTALLLPLALLLHAARPMGRGLLRGLWPLHIVLWTRIASTIP
MALPVTALLLPLALLLHAARPMGRGLLRGLWPLHIVLWTRIASTIP
MALPVTALLLPLALLLHAARPQLCKFCDVRFSTCDNQKSCMSNCSI
MALPVTALLLPLALLLHAARPQLCKFCDVRFSTCDNQKSCMSNCSI
MALPVTALLLPLALLLHAARPQLCKFCDVRFSTCDNQKSCMSNCSI
MALPVTALLLPLALLLHAARPQLCKFCDVRFSTCDNQKSCMSNCSI
MALPVTALLLPLALLLHAARPQLCKFCDVRFSTCDNQKSCMSNCSI
MALPVTALLLPLALLLHAARPSDPTRVETATETAWISLVTALLLVLG
MALPVTALLLPLALLLHAARPSDPTRVETATETAWISLVTALHLVL
GLNAVLGLLLLRKQFPAHYRRLRHALWPSLPDLHRVLGQYLRDTA
ALSPPRATVSDTCEEVEPSLLEILPRSSERTPLPLLEDEGVAGAPTGS
MALPVTALLLPLALLLHAARP
PGWFLDSPDRPWNPPTFSPALLVV
TEGDNATFTCSFSNTSESFHVIWHRESPSGQTDTLAAFPEDRSQP
GQDCRFRVTQLPNGRDFHMSVVRARRNDSGTYVCGVISLAPKIQI
KESLRAELRVTERRAEVPTAHPSPSPRPAGQFQTLVSDPTRVETAT
MALPVTALLLPLALLLHAARP
PGWFLDSPDRPWNPPTFSPALLVV
TEGDNATFTCSFSNTSESFHVIWHRESPSGQTDTLAAFPEDRSQP
GQDCRFRVTQLPNGRDFHMSVVRARRNDSGTYVCGVISLAPKIQI
KESLRAELRVTERRAEVPTAHPSPSPRPAGQFQTLVSDPTRVETAT
F. Expression of Chimeric Cytokine Receptors
Provided herein are polynucleotides encoding any one of the chimeric cytokine receptors provided herein. Likewise, provided herein are expression vectors comprising such polynucleotides. In some embodiments, the vector is a viral vector. In some embodiments, the vector is not a viral vector.
In some embodiments, the vector comprises a polynucleotide encoding a chimeric cytokine receptor, and a polynucleotide expressing a chimeric antigen receptor (CAR).
In some embodiments, expression of the chimeric cytokine receptor and the CAR are expressed as a single polypeptide chain, separated by a linker.
Provided herein are engineered immune cells comprising a polynucleotide encoding a chimeric antigen receptor and a chimeric cytokine receptor of the disclosure; and provided herein are engineered immune cells expressing a chimeric antigen receptor (CAR-I cell) and a chimeric cytokine receptor of the disclosure. Examples of immune cells include T-cells, e.g., alpha/beta T-cells and gamma/delta T-cells, B cells, natural killer (NK) cells, natural killer T (NKT) cells, invariant NKT cells, mast cells, myeloid-derived phagocytes, dendritic cells, killer dendritic cells, macrophages, and monocytes. Immune cells also refer to cells derived from, for example without limitation, a stem cell. The stem cells can be adult stem cells, non-human embryonic stem cells, more particularly non-human stem cells, cord blood stem cells, progenitor cells, bone marrow stem cells, induced pluripotent stem cells, totipotent stem cells or hematopoietic stem cells.
Accordingly in some embodiments, provided herein are CAR-T cells comprising a chimeric cytokine receptor of the disclosure.
In some embodiments, a CAR can comprise an extracellular ligand-binding domain (e.g., a single chain variable fragment (scFv)), a transmembrane domain, and an intracellular signaling domain. In some embodiments, the extracellular ligand-binding domain, transmembrane domain, and intracellular signaling domain are in one polypeptide, i.e., in a single chain. Multichain CARs and polypeptides are also provided herein. In some embodiments, the multichain CARs comprise: a first polypeptide comprising a transmembrane domain and at least one extracellular ligand-binding domain, and a second polypeptide comprising a transmembrane domain and at least one intracellular signaling domain, wherein the polypeptides assemble together to form a multichain CAR.
The extracellular ligand-binding domain of a CAR specifically binds to a target of interest. The target of interest can be any molecule of interest, including, for example, without limitation any one or more of those presented in Table 8.
In some embodiments, the extracellular ligand-binding domain of a CAR comprises an scFv comprising the light chain variable (VL) region and the heavy chain variable (VH) region of a target antigen specific monoclonal antibody joined by a flexible linker. Single chain variable region fragments are made by linking light and/or heavy chain variable regions by using a short linking peptide (Bird et al., Science 242:423-426, 1988) (e.g. glycine-serine containing linkers). In general, linkers can be short, flexible polypeptides and are generally comprised of about 20 or fewer amino acid residues. Linkers can in turn be modified for additional functions, such as attachment of drugs or attachment to solid supports. The single chain variants can be produced either recombinantly or synthetically. For synthetic production of scFv, an automated synthesizer can be used. For recombinant production of scFv, a suitable plasmid containing polynucleotide that encodes the scFv can be introduced into a suitable host cell, either eukaryotic, such as yeast, plant, insect or mammalian cells, or prokaryotic, such as E. coli. Polynucleotides encoding the scFv of interest can be made by routine manipulations such as ligation of polynucleotides. The resultant scFv can be isolated using standard protein purification techniques known in the art.
The intracellular signaling domain of a CAR according to the invention is responsible for intracellular signaling following the binding of extracellular ligand-binding domain to the target resulting in the activation of the immune cell and immune response (Signals 1 and/or 2). The intracellular signaling domain has the ability to activate at least one of the normal effector functions of the immune cell in which the CAR is expressed. For example, the effector function of a T cell can be a cytolytic activity or helper activity including the secretion of cytokines.
In some embodiments, an intracellular signaling domain for use in a CAR can be the cytoplasmic sequences of, for example without limitation, the T cell receptor and co-receptors that act in concert to initiate signal transduction following antigen receptor engagement, as well as any derivative or variant of these sequences and any synthetic sequence that has the same functional capability. Intracellular signaling domains comprise two distinct classes of cytoplasmic signaling sequences: those that initiate antigen-dependent primary activation, and those that act in an antigen-independent manner to provide a secondary or co-stimulatory signal. Primary cytoplasmic signaling sequences can comprise signaling motifs which are known as immunoreceptor tyrosine-based activation motifs of ITAMs. ITAMs are well defined signaling motifs found in the intracytoplasmic tail of a variety of receptors that serve as binding sites for syk/zap70 class tyrosine kinases. Examples of ITAM used in the invention can include as non-limiting examples those derived from TCRξ, FcRγ, FcRβ, FcRε, CD3γ, CD3δ, CD3ε, CD5, CD22, CD79a, CD79b and CD66d. In some embodiments, the intracellular signaling domain of the CAR can comprise the CD3ξ signaling domain. In some embodiments the intracellular signaling domain of the CAR of the invention comprises a domain of a co-stimulatory molecule.
In some embodiments, the intracellular signaling domain of a CAR of the invention comprises a part of co-stimulatory molecule selected from the group consisting of fragment of 41BB (GenBank: AAA53133.) and CD28 (NP_006130.1).
CARs are expressed on the surface membrane of the cell. Thus, the CAR comprises a transmembrane domain. Suitable transmembrane domains for a CAR disclosed herein have the ability to (a) be expressed at the surface of a cell, preferably an immune cell such as, for example without limitation, lymphocyte cells or Natural killer (NK) cells, and (b) interact with the ligand-binding domain and intracellular signaling domain for directing cellular response of immune cell against a predefined target cell. The transmembrane domain can be derived either from a natural or from a synthetic source. The transmembrane domain can be derived from any membrane-bound or transmembrane protein. As non-limiting examples, the transmembrane polypeptide can be a subunit of the T cell receptor such as α, β, γ or δ, polypeptide constituting CD3 complex, IL-2 receptor p55 (a chain), p75 (β chain) or γ chain, subunit chain of Fc receptors, in particular Fcγ receptor III or CD proteins. Alternatively, the transmembrane domain can be synthetic and can comprise predominantly hydrophobic residues such as leucine and valine. In some embodiments said transmembrane domain is derived from the human CD8a chain (e.g., NP_001139345.1). The transmembrane domain can further comprise a stalk domain between the extracellular ligand-binding domain and said transmembrane domain. A stalk domain may comprise up to 300 amino acids, preferably 10 to 100 amino acids and most preferably 25 to 50 amino acids. Stalk region may be derived from all or part of naturally occurring molecules, such as from all or part of the extracellular region of CD8, CD4, or CD28, or from all or part of an antibody constant region. Alternatively the stalk domain may be a synthetic sequence that corresponds to a naturally occurring stalk sequence, or may be an entirely synthetic stalk sequence. In some embodiments said stalk domain is a part of human CD8a chain (e.g., NP_001139345.1). In another particular embodiment, said transmembrane and hinge domains comprise a part of human CD8a chain. In some embodiments, CARs disclosed herein can comprise an extracellular ligand-binding domain that specifically binds BCMA, CD8a human hinge and transmembrane domains, the CD3(signaling domain, and 4-1BB signaling domain.
In some embodiments, a CAR can be introduced into an immune cell as a transgene via a plasmid vector. In some embodiments, the plasmid vector can also contain, for example, a selection marker which provides for identification and/or selection of cells which received the vector.
Table 7 provides exemplary sequences of CAR components that can be used in the CARs disclosed herein.
In some embodiments, the CAR-immune cell (e.g., CAR-T cell) of the disclosure comprises a polynucleotide encoding a suicide polypeptide, such as for example RQR8. See, e.g., WO2013153391A, which is hereby incorporated by reference in its entirety. In some embodiments, a suicide polypeptide is expressed on the surface of the cell. In some embodiments, a suicide polypeptide is included in the CAR construct. In some embodiments, a suicide polypeptide is not part of the CAR construct.
In some embodiments, the extracellular domain of any one of CARs disclosed herein may comprise one or more epitopes specific for (specifically recognized by) a monoclonal antibody. These epitopes are also referred to herein as mAb-specific epitopes. Exemplary mAb-specific epitopes are disclosed in International Patent Publication No. WO 2016/120216, which is incorporated herein in its entirety. In these embodiments, the extracellular domains of the CARs comprise antigen binding domains that specifically bind to a target of interest and one or more epitopes that bind to one or more monoclonal antibodies (mAbs). CARs comprising the mAb-specific epitopes can be single-chain or multi-chain.
The inclusion of epitopes specific for monoclonal antibodies in the extracellular domain of the CARs described herein allows sorting and depletion of engineered immune cells expressing the CARs. In some embodiments, allowing for depletion provides a safety switch in case of deleterious effects, e.g., upon administration to a subject.
Methods of preparing immune cells for use in immunotherapy are also provided herein. In some embodiments, the methods comprise introducing a chimeric cytokine receptor and a CAR into immune cells, and expanding the cells. In some embodiments, the invention relates to a method of engineering an immune cell comprising: providing a cell and expressing a chimeric cytokine receptor, and expressing at the surface of the cell at least one CAR. In some embodiments, the method comprises: transfecting the cell with at least one polynucleotide encoding a chimeric cytokine receptor, and at least one polynucleotide encoding a CAR, and expressing the polynucleotides in the cell. In some embodiments, the method comprises: transfecting the cell with at least one polynucleotide encoding a chimeric cytokine receptor, at least one polynucleotide encoding a CAR, and expressing the polynucleotides in the cell. In some embodiments, the chimeric cytokine receptor and the CAR reside on one polynucleotide.
In some embodiments, the one or more polynucleotides encoding the chimeric cytokine receptor and CAR are present in one or more expression vectors for stable expression in the cells. In some embodiments, the polynucleotides are present in viral vectors for stable expression in the cells. In some embodiments, the one or more polynucleotides are inserted into the cellular genome by random integration, and in other embodiments, inserted into specific locations of the cellular genome by site-specific integration. In some embodiments, the viral vectors may be for example, lentiviral vectors or adenoviral vectors. In some embodiments, the one or more polynucleotides are present in non-viral vectors.
In some embodiments, polynucleotides encoding polypeptides according to the present disclosure can be mRNA which is introduced directly into the cells, for example by electroporation. In some embodiments, CytoPulse electroporation technology, such as PulseAgile, can be used to transiently permeabilize living cells for delivery of material into the cells (e.g. U.S. Pat. No. 6,078,490; PCT/US2011/000827; and PCT/US2004/005237). Parameters can be modified in order to determine conditions for high transfection efficiency with minimal mortality.
Also provided herein are methods of transfecting an immune cell, e.g a T-cell. In some embodiments, the method comprises: contacting a T-cell with RNA and applying to the T-cell an agile pulse sequence. In some embodiments, a method of transfecting an immune cell (e.g. T-cell) comprising contacting the immune cell with RNA and applying to the cell an agile pulse sequence.
In some embodiments, the method can further comprise a step of genetically modifying a cell by inactivating at least one gene expressing, for example without limitation, a component of the TCR, a target for an immunosuppressive agent, an HLA gene, and/or an immune checkpoint protein such as, for example, PDCD1 or CTLA-4. By inactivating a gene it is intended that the gene of interest is not expressed in a functional protein form. In some embodiments, the gene to be inactivated is selected from the group consisting of, for example without limitation, TCRα, TCRβ, CD52, GR, deoxycytidine kinase (DCK), TGF-B, and CTLA-4. In some embodiments the method comprises inactivating one or more genes by introducing into the cells a rare-cutting endonuclease able to selectively inactivate a gene by selective DNA cleavage. In some embodiments the rare-cutting endonuclease can be, for example, a transcription activator-like effector nuclease (TALE-nuclease) or CRISPR-based endonuclease (e.g Cas-9 or Cas12a).
In another aspect, a step of genetically modifying cells can comprise: modifying immune cells (e.g. T-cells) by inactivating at least one gene expressing a target for an immunosuppressive agent, and; expanding the cells, optionally in presence of the immunosuppressive agent.
In some embodiments, the engineered immune cells (e.g. T-cells) provided herein exhibit improved cytotoxicity, increased expansion, and/or increased levels of memory phenotype markers upon contact with a TGF-β ligand or anti-TGF-β-receptor antibody that binds to the binding domain of the chimeric cytokine receptor relative to engineered immune cells that do not express the chimeric cytokine receptor.
In some embodiments, the engineered immune cells (e.g. T-cells) provided herein exhibit (i) increased in vivo persistence, (ii) increased STAT activation, (iii) increased cytotoxicity, (iv) increased levels of memory phenotype markers, (v) increased expansion (proliferation), or combinations of these functional features, upon contact with a TGF-β ligand or anti-TGF-β-receptor antibody that binds to the binding domain of the chimeric cytokine receptor relative to engineered immune cells that do not express the chimeric cytokine receptor. In some embodiments, the improvement in the one or more functional features described herein is dose-dependent, i.e., the functional activity of the immune cell comprising the chimeric cytokine receptors increases upon contact with increasing doses of the PD-L1/PD-L2/TGF-B or an antibody to the respective receptor. In some embodiments, STATs activated by the engineered immune cell comprising one or more chimeric cytokine receptors disclosed are STAT1, STAT2, STAT3, STAT4, STAT5, STAT6, or combinations thereof. In one embodiment, memory phenotype markers that are increased or maintained by the immune cell comprising the chimeric cytokine receptor of the disclosure include stem cell memory (Tscm) markers and central memory (Tcm) markers.
In some embodiments, the improvement in one or more functional features exhibited by an engineered immune cell comprising a chimeric cytokine receptor provided herein is at least about 2 fold, 2.5 fold, 3 fold, 3.5 fold, 4 fold, 4.5 fold, 5 fold, 6 fold, 7 fold, 8 fold, 9 fold, 10 fold, 15 fold, 20 fold, 25 fold, 30 fold, 40 fold, 50 fold, 60 fold, 70 fold, 80 fold, 90 fold, 100 fold, 125 fold, 150 fold, 200 fold, 250 fold, 300 fold, 350 fold, 400 fold, 450 fold, or even about 10-500 fold, including values and ranges therebetween, compared to an immune cell that does not express the chimeric cytokine receptor.
In some embodiments, the improvement in one or more functional features exhibited by an engineered immune cell comprising a chimeric cytokine receptor provided herein is at least about 10%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 70%, 75%, 80%, 90%, 100%, 125%, 150%, 200%, 250%, 300%, 350%, 400%, or even about 80%-500%, including values and ranges therebetween, compared to an engineered immune cell that does not express the chimeric cytokine receptor.
Provided herein are pharmaceutical compositions comprising cells bearing the chimeric cytokine receptors and CARs of the disclosure.
Engineered chimeric cytokine receptor-bearing and CAR-bearing immune cells (e.g. T-cells) obtained by the methods described above, or cell lines derived from such engineered immune cells, can be used as a medicament. In some embodiments, such a medicament can be used for treating a disorder such as for example a viral disease, a bacterial disease, a cancer, an inflammatory disease, an immune disease, or an aging—associated disease. In some embodiments, the cancer is a solid cancer. In some embodiments the cancer is a liquid cancer. The cancer can be selected from the group consisting of gastric cancer, sarcoma, lymphoma, leukemia, head and neck cancer, thymic cancer, epithelial cancer, salivary cancer, liver cancer, stomach cancer, thyroid cancer, lung cancer, small cell lung cancer, ovarian cancer, breast cancer, prostate cancer, esophageal cancer, pancreatic cancer, glioma, glioblastoma, leukemia, multiple myeloma, renal cell carcinoma, bladder cancer, cervical cancer, choriocarcinoma, colon cancer, oral cancer, skin cancer, and melanoma. In some embodiments, the subject is a previously treated adult subject with locally advanced or metastatic melanoma, squamous cell head and neck cancer (SCHNC), ovarian carcinoma, sarcoma, or relapsed or refractory classic Hodgkin's Lymphoma (cHL).
In some embodiments, engineered immune cells, or cell line derived from the engineered immune cells, can be used in the manufacture of a medicament for treatment of a disorder in a subject in need thereof. In some embodiments, the disorder can be, for example, a cancer, an autoimmune disorder, or an infection.
Also provided herein are methods for treating subjects in need of such treatment.
As used herein, the term “subject” refers to any vertebrate including, without limitation, humans and other primates (e.g., chimpanzees, cynomologous monkeys, and other apes and monkey species), farm animals (e.g., cattle, sheep, pigs, goats and horses), domestic mammals (e.g., dogs and cats), laboratory animals (e.g., rabbits, rodents such as mice, rats, and guinea pigs), and birds (e.g., domestic, wild and game birds such as chickens, turkeys and other gallinaceous birds, ducks, geese, and the like). In some embodiments, the subject is a mammal. In exemplary embodiments, the subject is a human.
In some embodiments the method comprises providing immune cells of the disclosure, bearing the chimeric cytokine receptors and CARs described herein to a subject in need thereof.
In some embodiments, chimeric cytokine receptor and CAR-bearing T-cells of the invention can undergo robust in vivo T-cell expansion and can persist for an extended amount of time.
Methods of treatment of the invention can be ameliorating, curative or prophylactic. The method of the invention may be either part of an autologous immunotherapy or part of an allogenic immunotherapy treatment.
In another aspect, the invention provides a method of inhibiting tumor growth or progression in a subject who has a tumor, comprising administering to the subject an effective amount of chimeric cytokine receptor-expressing and CAR-expressing immune cells as described herein. In another aspect, the invention provides a method of inhibiting or preventing metastasis of cancer cells in a subject, comprising administering to the subject in need thereof an effective amount of engineered immune cells as described herein. In another aspect, the invention provides a method of inducing tumor regression in a subject who has a tumor, comprising administering to the subject an effective amount of engineered immune cells as described herein. In some embodiments, the subject is further administered with an anti-TGF-βR antibody, in particular, an anti-TGF-βR2 antibody.
In some embodiments, the engineered T-cells herein can be administered parenterally in a subject. In some embodiments, the engineered T-cells disclosed herein can be administered intravenously in a subject.
Also provided is the use of any of the engineered T-cells provided herein in the manufacture of a medicament for the treatment of cancer or for inhibiting tumor growth or progression in a subject in need thereof.
In some embodiments, treatment can be administrated into subjects undergoing an immunosuppressive treatment. Indeed, the invention preferably relies on cells or population of cells, which have been made resistant to at least one immunosuppressive agent due to the inactivation of a gene encoding a receptor for such immunosuppressive agent. In this aspect, the immunosuppressive treatment should help the selection and expansion of the T-cells according to the invention within the subject. The administration of the cells or population of cells according to the invention may be carried out in any convenient manner, including by aerosol inhalation, injection, ingestion, transfusion, implantation or transplantation. The compositions described herein may be administered to a subject subcutaneously, intradermally, intratumorally, intranodally, intramedullary, intramuscularly, by intravenous or intralymphatic injection, or intraperitoneally. Cells bearing the chimeric cytokine receptors and/or CARs of the disclosure or the pharmaceutical compositions thereof may be administered via one or more of the following routes of administration: intravenous, intraocular, intravitreal, intramuscular, subcutaneous, topical, oral, transdermal, intraperitoneal, intraorbital, by implantation, by inhalation, intrathecal, intraventricular, via the ear, or intranasal.
In some embodiments the administration of the cells or population of cells (bearing the chimeric cytokine receptors and CARs of the disclosure) can comprise administration of, for example, about 104 to about 109 cells per kg body weight including all integer values of cell numbers within those ranges. In some embodiments the administration of the cells or population of cells can comprise administration of about 104 to 105 cells per kg body weight, 105 to 106 cells per kg body weight, 106 to 107 cells per kg body weight, 107 to 108 cells per kg body weight, or 108 to 109 cells per kg body weight. The cells or population of cells can be administrated in one or more doses. In some embodiments, said effective amount of cells can be administrated as a single dose. In some embodiments, said effective amount of cells can be administrated as more than one dose over a period time. Timing of administration is within the judgment of managing physician and depends on the clinical condition of the subject. The cells or population of cells may be obtained from any source, such as a blood bank or a donor. While individual needs vary, determination of optimal ranges of effective amounts of a given cell type for a particular disease or condition is within the skill of the art. An effective amount means an amount which provides a therapeutic or prophylactic benefit. The dosage administrated will be dependent upon the age, health and weight of the recipient, kind of concurrent treatment, if any, frequency of treatment and the nature of the effect desired. In some embodiments, an effective amount of cells or composition comprising those cells are administrated parenterally. In some embodiments, administration can be an intravenous administration. In some embodiments, administration can be directly done by injection within a tumor.
The methods can further comprise administering one or more agents to a subject prior to administering the engineered immune cells bearing a CAR and a chimeric cytokine receptor provided herein. In certain embodiments, the agent is a lymphodepleting (preconditioning) regimen. For example, methods of lymphodepleting a subject in need of such therapy comprise administering to the subject specified beneficial doses of cyclophosphamide (between 200 mg/m2/day and 2000 mg/m2/day, about 100 mg/m2/day and about 2000 mg/m2/day; e.g., about 100 mg/m2/day, about 200 mg/m2/day, about 300 mg/m2/day, about 400 mg/m2/day, about 500 mg/m2/day, about 600 mg/m2/day, about 700 mg/m2/day, about 800 mg/m2/day, about 900 mg/m2/day, about 1000 mg/m2/day, about 1500 mg/m2/day or about 2000 mg/m2/day) and specified doses of fludarabine (between 20 mg/m2/day and 900 mg/m2/day, between about 10 mg/m2/day and about 900 mg/m2/day; e.g., about 10 mg/m2/day, about 20 mg/m2/day, about 30 mg/m2/day, about 40 mg/m2/day, about 40 mg/m2/day, about 50 mg/m2/day, about 60 mg/m2/day, about 70 mg/m2/day, about 80 mg/m2/day, about 90 mg/m2/day, about 100 mg/m2/day, about 500 mg/m2/day or about 900 mg/m2/day). An exemplary dosing regimen involves treating a subject comprising administering daily to the patient about 300 mg/m2/day of cyclophosphamide in combination or before or after administering about 30 mg/m2/day of fludarabine for three days prior to administration of a therapeutically effective amount of engineered immune cells to the patient.
In some embodiments, notably in the case when the engineered cells provided herein have been gene edited to eliminate or minimize surface expression of CD52, lymphodepletion further comprises administration of an anti-CD52 antibody, such as alemtuzumab. In some embodiments, the CD52 antibody is administered at a dose of about 1-20 mg/day IV, e.g., about 13 mg/day IV for 1, 2, 3 or more days. The antibody can be administered in combination with, before, or after administration of other elements of a lymphodepletion regime (e.g., cyclophosphamide and/or fludarabine).
In certain embodiments, compositions comprising CAR-expressing immune effector cells disclosed herein may be administered in conjunction with any number of chemotherapeutic agents.
The present disclosure provides kits comprising any one or more of the chimeric cytokine receptors and chimeric cytokine receptor-bearing cells described herein, and pharmaceutical compositions thereof. The present disclosure also provides articles of manufacture comprising any one or more of the chimeric cytokine receptors and chimeric cytokine receptors-bearing CAR-I-cells described herein, pharmaceutical compositions thereof, and kits described herein.
The following examples are included for illustrative purposes and are not intended to limit the scope of the disclosure.
All patent and non-patent documents referenced throughout this disclosure are incorporated by reference herein in their entirety for all purposes.
A HEK293T cell reporter assay was used to test the inducibility and magnitude of cytokine signaling using chimeric cytokine receptors for either neutralizing the TGF-β signaling or activating the STAT response, which can be used as a surrogate measurement for the cytokine ICD activation and cytokine signaling. Briefly, 20,000 HEK293T-cells were plated into each well of a poly-L-lysine-coated 96-well flat-bottom plate and cultured overnight at 37° C. with 5% CO2. A chimeric cytokine receptor-CAR construct (2.5 ng), a TGF-β or STAT-response element that drives Firefly Luciferase (100 ng; Promega), and Renilla Luciferase control reporter vector (1 ng; Promega) were mixed to a final volume of 5 μl in Opti-MEM (Gibco) (“DNA mix”).
Cells were transfected with a BFP-EGFRvIII CAR construct where a BFP gene is in place of the chimeric cytokine receptor as a negative control. A dominant negative truncation of TGFβR2 (“TGFβR2 DN”) and a dominant negative truncation of TGFβ1 (“TGFβR1 DN”) were also constructed as additional controls to examine dominant negative effects in the absence of an intracellular cytokine signal. After incubating the DNA mixes with premixed 0.3 μl Lipofectamine 2000 (Invitrogen) and 5 μl Opti-MEM at room temperature for 20 minutes, the mixture having a total volume of 10 μl was added to each well containing HEK293T cells. One day after transfection, a commercially available TGF-β1 ligand (BioLegend, hereinafter in Examples 1-4 referred to as “TGF-β”) was added to the culture for stimulation, to various final concentrations. After 20-24 hours of stimulation, TGF-β or STAT5 reporter activity was evaluated using the Dual-Glo Luciferase Assay System (Promega). Fold induction of TGF-β or STAT5 reporter activity was normalized to that of HEK293T cells that were transfected with only a reporter vector, and left untreated.
A chimeric cytokine receptor was constructed, as briefly described when referring to
Again, additional truncations (N-10, N-11, N-12, etc.) in the TM domain of TpoR cassette were designed (as shown in Table 3), and their capacity to regulate cytokine signaling was determined.
In the absence of TGFβR2, TGFβR1 interacts with the TGF-β ligand with very low affinity. Once the ECD of TGFβR2 binds to the TGF-β ligand, the binary complex has an extended interface to efficiently recruit TGFβR1 to form the ternary complex. The engineered TGFβR2 chimeric cytokine receptor can also engage endogenous TGFβR1, which may sterically intervene the intended signaling though the cytokine receptor ICDs. To abrogate interaction between the TGFβR2 chimeric cytokine receptors and TGFβR1, several variants for the TGFβR1 cassette were designed, and modifications that can enhance cytokine signaling while inhibiting the TGF-β signaling were identified.
It was determined that the truncation in the TGFβR2 binding domain enhances the cytokine signaling by 5-10 fold, even in the absence of a TGF-β ligand. Interestingly, the ΔN25 truncation was able to enhance the signaling synergistically with the TpoR TM truncations (e.g. N-7, N-8, N-9 and N+4). This combinatorial use of the TGFβR2 binding domain and TpoR TM truncation mutants represents a novel approach for simultaneously inhibiting immunosuppressive TGF-β signaling while transmitting immune-potentiating cytokine signaling.
We next tested the constitutive chimeric receptors in CAR T cells. All constructs tested in
The data in
Next, we compared the expression of TGF-βR2 chimeric cytokine receptor to the expression of endogenous TGF-βR2 by measuring total surface ECD by flow cytometry using an anti-human TGF-βR2 polyclonal antibody (R&D Systems, FAB2411A100). The results in
We next evaluated anti-tumor activities of the EGFRvIII CAR T cells expressing different chimeric cytokine receptors or controls against the target cells U87-EGFRvIII cells. In brief, CAR T cells were incubated with 10,000 target cells at E: T ratio of 1:2 in 200 ul of RPMI medium with 10% of FBS, and TGF-β at various concentrations of 0, 5, and 20 ng/ml. After one week of co-culture with target cells, the CAR T cells in 100 ul supernatant were transferred into new target cells (10,000) with the same TGFβ concentrations as the previous week. The cytotoxicity of the CAR T cells in the second week without added TGF-β was assessed and the results are shown in
We next evaluated further modified constitutive TGF-βR2 chimeric cytokine receptor in CAR T cells. As shown above constitutive TGFβR2.IL7IL12 chimeric cytokine receptor having the S505N/W515K substitutions in the TPOR/MPLR transmembrane domain and the IL7Ra/IL12Rb recruiting domains (e.g., SEQ ID NO:163) increased STAT5 phosphorylation and led to substantial differentiation of central memory T cells. As the IL12 cytokine signaling has been implicated in the differentiation of memory T cells, we designed the TGF-βR2.IL7 chimeric cytokine receptor that eliminates the IL12 signaling. In addition, we introduced two mutations in the TpoR JAK-binding domain, K553R and K573R, (designated as “RR”, e.g., SEQ ID NOS:165 and 170), to decrease ubiquitin-induced receptor degradation. See Saur S J, Sangkhae V, Geddis A E, Kaushansky K, Hitchcock IS. Ubiquitination and degradation of the thrombopoietin receptor c-Mpl. Blood. 2010. doi:10.1182/blood-2009-06-227033. CAR T cells expressing the chimeric cytokine receptor were produced and evaluated for STAT5 phosphorylation and T cell differentiation. Similar as before, these further modified TGF-βR2 chimeric cytokine receptors showed higher levels of STAT5 signaling as determined by STAT5 phosphorylation than the chimeric cytokine receptors without the TGF-βR2 ECD domain (both the IL7IL12 and IL7 chimeric cytokine receptor constructs contain the S505N/W515K substitutions) (
To evaluate how the TGF-βR2 chimeric cytokine receptors affect T cell functions, CAR T cells were evaluated in long-term killing assay. In brief, CAR T cells expressing different chimeric cytokine receptor were mixed with 10,000 U87-EGFRvIII cancer cells at an E:T ratio of 1:1, in 200 ul RPMI medium with 10% FBS, with or without 5 ng/ml of TGFβ. Every two or three days, 100 ul of the supernatant with CAR T cells were transferred onto 10,000 fresh target cells to the final volume of 200 ul RPMI medium with 10% FBS and 5 ng/ml of TGFβ, and the survival of old target cells were quantified. The long-term cytotoxicity of CAR T cells with different TGF-βR2 chimeric cytokine receptors are summarized in
To further assess the inhibition on TGFβ signaling by a TGF-βR2 chimeric cytokine receptor and its influence on the functionality of CAR T cells, we analyzed the TGF-βR2.IL2YY_RR chimeric cytokine receptor (SEQ ID NO: 166), which carries the dimerization mutations in the TM region (S505N, W515K) and the degradation-resistant mutations (K553R and K573R) in the JAK-binding domain. We designed two additional variants bearing mutations in the TGF-βR2 ECD (D32A.E119A and D32A.E119A.I53A) that abolished the receptor's ability to bind the TGFβ ligand. CAR T cells expressing the designated chimeric cytokine receptors were produced and evaluated for cytokine signaling (pSTAT5), TGFβ signaling (pSMAD), and persistency of cytotoxicity against U87-EGFRvIII target cells.
The long-term cytotoxicity of CAR T cells expressing different TGF-βR2 chimeric cytokine receptor against cancer cells in the presence of 5 ng/ml TGFβ was shown in
Results in
The present application claims the benefit of priority to U.S. Provisional Application No. 62/894,658, filed on Aug. 30, 2019; and U.S. Provisional Application No. 63/053,322, filed on Jul. 17, 2020, the contents of both of which are hereby incorporated by reference in their entireties.
| Number | Date | Country | |
|---|---|---|---|
| 63053322 | Jul 2020 | US | |
| 62894658 | Aug 2019 | US |
