Patent Application
20240424136
Biological products (biologics) as defined by the U.S. Food and Drug Administration include vaccines, blood and blood components, allergens, somatic cells, gene therapy, tissues, and recombinant therapeutic proteins. Cells from the same subject (autologous), from a subject of the same species (homologous or allogenic), or even from a different species (heterologous) can be administered to a subject as a biologic. In adoptive cell therapy (“ACT”), for example, T cells originating from a subject (or sometimes from a different source) are removed, genetically engineered to address the specific needs of the same or different subject, and then transferred back into the same or different subject. There are currently obstacles to widespread adoption and success of biologics such as ACT, however. Maintaining therapeutically effective levels of a biologic administered to a patient can be difficult, as the biologic may be expressed by an engineered cell at toxic levels or may be present or expressed for an unacceptably sustained duration. There is therefore a need for regulation of the biologics for optimization of therapeutic benefits and to facilitate widespread adoption of biologic therapies.
This disclosure relates to compositions and systems capable of regulating payload function, and methods of making and using the compositions and systems. Payload function can be regulated by modifying and/or modulating, among other things, abundance and/or activity of the payload. Described herein are compositions and systems capable of modifying and/or modulating payload activity and/or abundance, as well as methods of making and using the compositions and systems.
The present disclosure provides compositions, referred to as “modulation hubs,” comprising two or more drug responsive domains (“DRD”). DRDs are polypeptides that can regulate the abundance, availability, and/or activity of a payload under appropriate conditions, for example, in response to a small molecule ligand. In some embodiments, modulation hubs comprise DRDs linked in series by way of covalent bonds. In such embodiments, the DRDs are directly linked or indirectly linked, for example, through linkers or hinges. In certain embodiments, the modulation hubs comprise DRDs associated in oligomers (also referred to as multimeric fusion compositions or fusion compositions) of at least two DRD-oligomerization domain constructs, wherein the DRD-oligomerization domain constructs each comprise a DRD linked, directly or indirectly, to an oligomerization domain configured to promote oligomerization of the DRD-oligomerization domain constructs. In some embodiments, wherein the oligomerization domain is a trimerizing domain, the multimeric fusion compositions include three DRD-oligomerization domain constructs resulting in a modulation hub having at least three DRDs and three trimerizing domains. In any of the embodiments of the modulation hub, the DRDs in the modulation hub may all be the same, may all be different, or some may be the same and some may be different.
The present disclosure also provides compositions referred to as polypeptide monomers comprising an oligomerization domain configured to promote oligomerization of the polypeptide monomer; and, at least one payload having a biological activity under appropriate conditions, or at least one drug responsive domain (DRD) responsive to a ligand. In some embodiments, the regulatable polypeptide monomers comprise an oligomerization domain configured to promote oligomerization of the polypeptide, at least one payload having a biological activity level under appropriate conditions, and at least one drug responsive domain. In some such embodiments, for example those involving the same monomers, multiple monomers oligomerize to form an oligomer comprising at least two payloads operably linked to a modulation hub, which in turn comprises at least two oligomerization domains and at least two DRDs. In other embodiments, for example those involving different monomers, the multiple monomers oligomerize to form an oligomer comprising at least one payload operably linked to a modulation hub, which in turn comprises at least two oligomerization domains and at least two DRDs. In certain embodiments, regulation of payload abundance and/or function in the resultant oligomer is improved as compared to the same payload in a control construct. For example, in certain embodiments, the level of activity of the payload in the oligomer has a range spanning from a basal level of activity in the absence of ligand to a maximum activity level in the presence of a saturating amount of ligand and the basal activity level of the payload in the oligomer is less than that of the same payload in a control construct. In certain embodiments, the range of activity of the payload in the oligomer is greater than the range of activity of the same payload in a control construct. Thus, a better dose response is provided in the presence of the small molecule ligand specific for the DRD.
Also described herein are engineered, regulatable oligomers comprising at least two polypeptide monomers, wherein each monomer comprises an oligomerization domain configured to promote oligomerization of the monomers. Also described herein are engineered, regulatable oligomers comprising at least two polypeptide monomers, wherein each monomer comprises an oligomerization domain configured to promote oligomerization of the monomers, and at least one payload having a biological activity, or at least one DRD responsive to a ligand, or at least one payload having a biological activity and at least one DRD responsive to a ligand, provided that the oligomer comprises at least one payload and at least two DRDs. In some embodiments, the oligomer comprises at least two payloads and at least two DRDs. In some embodiments, the at least two payloads and the at least two DRDs are present in a 1:1 ratio.
In some embodiments, the engineered, regulatable oligomer comprises at least two polypeptide monomers, wherein each monomer comprises an oligomerization domain, at least one payload, and at least one DRD, such that the oligomer comprises at least two payloads operably linked to at least two DRDs. The oligomer can be formed by the same or different monomers, and each of those monomers can have one or more DRDs and/or one or more payloads. If a monomer has more than one DRD and/or more than one payload, the multiple DRDs and multiple payloads in the oligomer will be the same if the oligomer is formed from all the same monomers and all DRDs and all payloads in the monomer are the same. Alternatively, the multiple DRDs and multiple payloads in the oligomer will be different if the oligomer is formed from different monomers having different payloads and DRDs or the oligomer is formed from the same monomers, but each monomer has multiple different payloads and multiple different DRDs. In certain embodiments, the oligomer may have multiples of the same payload and multiple different DRDs or multiple different payloads and multiple of the same DRD.
These engineered, regulatable oligomers are optionally hetero-oligomers comprising either different DRDs, different payloads, or different DRDs and different payloads. In some hetero-oligomer embodiments, the oligomerization domain of one of the monomers is a hetero-oligomerization domain. In certain hetero-oligomer embodiments, the engineered, regulatable oligomer comprises at least two polypeptide monomers constituting a first, a second, and a third polypeptide monomer, wherein the first and second polypeptide monomers are the same, wherein each of the first and second polypeptide monomers comprises an oligomerization domain and a DRD, and wherein the third polypeptide monomer comprises a hetero-oligomerization domain and a payload.
In embodiments of the regulatable, engineered oligomers, regulation of function of a payload in the oligomer is improved as compared to the same payload in a control construct. For example, in certain embodiments, the biological activity of a payload in the engineered, regulatable oligomer has a range spanning from a basal level of activity in the absence of ligand to a maximum activity in the presence of a saturating amount of ligand and the basal activity level of the payload in the oligomer is less than that of the same payload in a control construct. In some embodiments, the range of biological activity of a payload in the oligomer is greater than the range of the same payload in a control construct.
Also provided are compositions referred to as engineered, regulatable polypeptides with at least one payload having a biological activity level and a modulation hub having at least two drug responsive domains (DRD), wherein the modulation hub is operably linked to the payload and wherein the at least two DRDs are responsive to a ligand. The biological activity of the payload is regulated by interaction of the at least two DRDs of the modulation hub with an effective amount of the ligand under appropriate conditions. In embodiments, regulation of function of the at least one payload within the polypeptide is improved as compared to the same payload in a control construct. For example, in some such embodiments, the activity of the at least one payload ranges from a basal activity level in the absence of the ligand to a maximum activity in the presence of a saturating amount of the ligand, and the basal activity of the at least one payload is lower than that of the same payload in a control construct. As another example, the range of activity level and the dose-response of the at least one payload in the engineered, regulatable polypeptide is optionally greater than that of the same payload in a control construct.
Provided herein are expressible nucleic acid constructs and vectors that encode one or more engineered, regulatable polypeptide monomers, which, when expressed, are capable of assembling into oligomers. Also provided are pluralities of nucleic acid constructs encoding the same or different engineered, regulatable polypeptide monomers such that, when expressed, assemble into oligomers, wherein the oligomers comprise at least one payload operably linked to a modulation hub comprising at least two DRDs. In embodiments the oligomers comprise at least two payloads operably linked to a modulation hub comprising at least two DRDs, wherein the ratio of payload:DRD is 1:1. The disclosure also provides nucleic acid constructs encoding engineered, regulatable polypeptides.
Cells containing one or more expressible nucleic acid constructs or vectors are also provided. Optionally, the cell is a human cell, for example, an immune cell.
The disclosure also provides systems for modifying and/or regulating (hereinafter “regulating”) the function of a payload, comprising a ligand and any of the referenced polypeptides, oligomers, nucleic acid constructs, vectors, or cells.
Disclosed herein are methods of regulating the function of a payload. In some embodiments, the method of regulation comprises engineering a cell to express a payload operably linked to a modulation hub comprising two or more DRDs. In such embodiments, the level of activity of the payload in the absence of ligand is reduced as compared to a control cell, for example, a cell engineered to express the payload independent of a DRD. Optionally, the method comprises contacting a cell engineered to express a payload operably linked to a modulation hub comprising two or more DRDs responsive to a ligand with an effective amount of the ligand such that the activity level of the payload is increased relative the basal activity level. Optionally, the two or more DRDs are responsive to the same ligand and the method comprises alternatively contacting the cell with a first selected dose of a ligand and a second selected dose of the same ligand, wherein the first and second selected dose of the ligand results in a selected activity level of the payload, the first and second selected dose of the ligand may be near zero and up to a saturating dose and may be the same or different. In embodiments wherein the modulation hub comprises a first DRD responsive to a first ligand and a second DRD responsive to a second ligand, and further wherein the first DRD is different from the second DRD and the first ligand is different from the second ligand, these embodiments optionally comprise contacting the hub with a selected amount of the first ligand and a selected amount of the second ligand, wherein the first ligand is different from the second ligand.
Disclosed herein are methods of controlling the dose or duration of administration of a payload to a subject, comprising administering to the subject one or more nucleic acid constructs, vectors, or cells as described herein. The method optionally further includes administering to the subject a selected amount of a ligand to deliver a selected activity of the payload to the subject thereby controlling the activity level of the payload administered by way of the one or more nucleic acid constructs, vectors or cells.
Also disclosed herein are methods of regulating expression of a downstream target protein or peptide of a gene editing process. Such methods can comprise engineering a cell to express an engineered, regulatable oligomer or polypeptide comprising a payload such as a CAS9 protein or transcription factor protein involved in controlling a gene editor, wherein the payload is operably linked to a modulation hub. In such methods, a nucleic acid construct or vector described herein is administered to a cell (in vivo, ex vivo, or in vitro) or a cell comprising the nucleic acid or vector is administered to a subject to regulate expression of the target protein or peptide.
The identified embodiments are exemplary only and are therefore non-limiting. The details of one or more non-limiting embodiments of the invention are set forth in the accompanying drawing and the description below. Other embodiments of the invention should be apparent to those of ordinary skill in the art after consideration of the present disclosure.
The present disclosure provides compositions and systems for regulatory control of a payload (“regulation compositions and systems”). Regulation compositions according to this disclosure include modulation hubs, wherein a modulation hub, comprises at least two drug responsive domains (DRDs) responsive to a ligand; and, at least one payload operably linked to the modulation hub. Regulation compositions also include engineered, regulatable polypeptide monomers (or polypeptide monomers, or simply, monomers); engineered, regulatable oligomers (or regulatable oligomers, or simply, oligomers); and engineered, regulatable polypeptides (or regulated polypeptides, or simply, polypeptides). The regulatable oligomers are formed from the regulatable monomers, and the regulatable oligomers and regulatable polypeptides comprise at least one payload operably linked to a modulation hub. Regulation systems according to this disclosure comprise the regulation compositions and a stabilizing ligand.
In some embodiments, this disclosure serves to enable regulation of a biologically active payload. For example, this disclosure describes improved drug responsive domain (DRD)-based regulation of payloads by improving control over the off-state of the payload (i.e., reducing the abundance or availability of the payload in the absence of ligand) and/or optimizing its range of regulation as compared to DRD-regulation systems comprising a single DRD.
Without meaning to be limited by theory, DRDs are thought to be unstable polypeptides that degrade in the absence of their corresponding stabilizing ligand (also referred to as the paired ligand or ligand), but whose stability is rescued by binding to the stabilizing ligand. Because binding of the ligand to the DRD is reversible, later removal of the ligand results in the DRD unfolding, becoming unstable, and ultimately being tagged for degradation by the ubiquitin-proteasome system (“UPS”). Accordingly, it is believed that when a DRD is operably linked to a payload, the entire construct (i.e., DRD plus payload) itself is rendered unstable and degraded by the UPS. However, in the presence of the paired ligand, the construct is stabilized, and the payload remains available for use. Further, it is believed that the conditional nature of DRD stability allows a rapid and non-perturbing switch from stable polypeptide to unstable UPS substrate, and may facilitate regulation of a payload's activity level, and/or modulation of a payload's activity level. The underlying discovery that led to the improved regulatory control is that multiple DRDs associated together in a modulation hub result in a payload having a lower off-state as compared to the same payload operably linked to a single DRD. That is, in the absence of ligand, increasing the density of DRDs (for example with multiple DRDs) is thought to reduce the abundance or availability of a payload as compared to a payload that is operably linked to only a single DRD.
Payloads should be understood to include one or more polypeptides having one or more functions, such as one or more biological activities, desired to be regulated. Payloads include multiple classes of therapeutically important polypeptides (proteins and peptides) such as Type I/II membrane proteins, cytokines, intracellular proteins, secreted proteins, CAS9 proteins, and transcription factor proteins.
Because the abundance and availability of a payload are related to the activity of a payload, for purposes of this disclosure, the terms “abundance,” “availability,” “activity,” and the phrase “abundance and/or activity” (and similarly “level of abundance,” “level of availability,” “level of activity,” and “level of abundance and/or activity”) are used interchangeably throughout this disclosure and are generally referred to as “activity,” unless explicitly stated otherwise or nonsensical in context. Further, measurements of abundance or availability are used as a proxy for activity level and may be used herein to reflect the activity level. Consequently, changes in the abundance or availability of a payload in the presence of an effective amount of ligand as compared to in the absence of ligand optionally serves as a proxy for measuring changes in activity level.
Provided herein are engineered, regulatable polypeptides having at least one payload and a modulation hub with at least two drug responsive domains (DRD), wherein the modulation hub is operably linked to the payload and wherein the at least two DRDs are responsive to a ligand. The at least two DRDs can be the same or different, and optionally the least two DRDs are responsive to the same ligand. For example, in certain embodiments, the modulation hub comprises three DRDs, wherein the three DRDs are responsive to the same ligand. The at least one payload has a biological activity, and the biological activity of the payload is regulated by interaction of the two or more DRDs (e.g., 2, 3, 4, or more, which are responsive to the same or different ligands) with an effective amount of the ligand. In the case of multiple different DRDs responsive to different ligands, it is understood that reference to “the ligand” means “the ligands.” The activity level of the at least one payload ranges from a basal activity level in the absence of the ligand to a maximum activity level in the presence of a saturating amount of the ligand, and the basal activity level of the payload in the regulatable polypeptide is lower than that of the same payload in a control construct. Saturating amount of the ligand refers to any amount of ligand at or above the amount that results in the maximum abundance and/or activity of the payload. By way of example, the activity level of the at least one payload ranges from a basal activity level in the absence of the ligand to a maximum activity level in the presence of a saturating amount of the ligand, and the range of activity level of the payload in the regulatable polypeptide is greater than that of the same payload in a control construct. In some embodiments, the at least one payload is multiple payloads (e.g., two payloads or three payloads, which are the same as or different from each other). Thus, for example, in some embodiments, the at least one payload is three payloads and the at least two DRDs is three DRDs, wherein the three payloads are the same and the three DRDs are responsive to the same ligand. In certain embodiments, the at least one payload is one payload and the at least two DRDs is three DRDs responsive to the same ligand.
Provided herein are engineered polypeptide monomers and engineered, regulatable oligomers of at least two engineered polypeptide monomers. Oligomers comprise at least one payload operably linked to a modulation hub comprising two or more DRDs. The payload has a biological activity, and the biological activity of the payload is regulated by interaction of the two or more DRDs (e.g., 2, 3, 4, or more, which are responsive to the same or different ligands) and an effective amount of the ligand.
In some embodiments, the monomers comprise at least one payload, an oligomerization domain (e.g., a dimerization domain, a trimerization domain, a tetramerization domain, a pentamerization domain, or a hexamerization domain) configured to promote oligomerization of the monomers, and at least one DRD responsive to a ligand, wherein the at least one payload is operably linked to the at least one DRD. In certain embodiments, the monomers comprise an oligomerization domain; and, at least one payload, or at least one DRD, or at least one payload and at least one DRD, provided that when at least two or more monomers oligomerize to form an oligomer, the resultant oligomer comprises at least one payload operably linked to a modulation hub comprising at least two DRDs.
Oligomers according to this disclosure are a multimeric association of at least two engineered, regulatable polypeptide monomers. The monomers of the oligomer associate through an oligomerization domain. The oligomer, for example, can be a dimer resulting from association of monomers via a dimerization domain; or it can be a trimer resulting from association of monomers via a trimerization domain; or it can be a tetramer resulting from association of monomers via a tetramerizing domain; or it can be a pentamer resulting from association of monomers via a pentamerizing domain; or it can be a hexamer resulting from association of monomers via a hexamerizing domain. In each case, the oligomer may result from monomers that are the same or different. Accordingly, the payload or payloads of each of the monomers is the same or different and the DRDs of each of the monomers is the same or different. Thus, by way of example, the oligomer can be an association of three monomers, wherein each monomer comprises the same payload, oligomerization domain, and DRD and consequently the oligomer comprises a first, second, and third payload that are the same and a modulation hub comprising a first, second, and third DRD that are responsive to the same ligand.
Thus, provided herein is also an engineered, regulatable oligomer comprising at least two polypeptide monomers, wherein each monomer comprises an oligomerization domain and at least one payload or one DRD, wherein the oligomer comprises at least one payload operably linked to at least two DRDs, wherein the at least one payload has a biological activity, wherein the at least two DRDs are responsive to a ligand. Optionally, the oligomer is a hetero-oligomer wherein the at least two polypeptide monomers of the hetero-oligomer each comprise an oligomerization domain and wherein in some embodiments the oligomerization domain of one of the polypeptide monomers comprises a hetero-oligomerization domain. Optionally the DRDs in the hetero-oligomer are the same or different. Optionally, the at least two DRDs are responsive to the same ligand. By way of example, the engineered, regulatable hetero-oligomer comprises a first, a second, and a third polypeptide monomer, wherein the first and second polypeptide monomers are the same, wherein each of the first and second polypeptide monomers comprises a DRD, and wherein the third polypeptide monomer comprises a hetero-oligomerization domain and a payload.
Multiple payloads in an oligomer can be the same or different, but in embodiments, each of the payload(s) has a biological activity under appropriate conditions. In some such embodiments, the level of activity of each payload in the oligomer has a range spanning from a basal level of activity in the absence of ligand to a maximum activity in the presence of a saturating amount of ligand, and the basal activity of each payload of the oligomer is less than that of the same payload in a control construct. In some embodiments, the range of activity of each payload in the oligomer is greater than that of the same payload in a control construct. See, e.g., examples 3-5 below.
Also provided are oligomers comprising at least two polypeptide monomers, wherein each monomer comprises at least one payload, an oligomerization domain, and one DRD, wherein the oligomer comprises at least two payloads operably linked to at least two DRDs, wherein the at least two payloads have a biological activity level, wherein the DRDs are responsive to a ligand, and wherein, in some embodiments, the at least two payloads and the at least two DRDs are present in a 1:1 ratio. In certain embodiments, the payload is present in a an oligomer in a 1:2, a 1:3, a 2:3, a 1:4, a 3:4, a 1:5, a 2:5, a 3:5 or a 4:5 ratio of payload to DRD or in a 2:1, 3:1, 3:2, 4:1, 4:3, 5:1, 5:2, 5:3 or 5:4 ratio of DRD to payload (provided that the oligomer always comprises at least two DRDs). In some embodiments, the at least two DRDs may be the same or different, the at least one payload is multiple payloads, which may be the same or different, or the multiple DRDs may be different but responsive to the same ligand. The oligomer can include, for example, a modulation hub comprising a first, second, and third DRD, which are responsive to the same or different ligands, and a first, second, and third payload that are the same or different. In some embodiments, the first, second, and third DRD are responsive to the same ligand and the first, second and third payloads are the same. The level of activity of each payload in the oligomer has a range spanning from a basal level of activity in the absence of ligand to a maximum activity in the presence of a saturating amount of ligand and wherein the basal activity of each payload in the oligomer is less than that of the same payload in a control construct. Optionally, the range of activity level of the payload in the oligomer is greater than that of the same payload in a control construct.
Example components (building blocks) of the engineered monomers which associate to form regulatable, engineered oligomers, and of the engineered, regulatable polypeptides described herein are referenced throughout this disclosure and provided below. As described herein, monomers include at least an oligomerization domain and: a payload, or DRD, or a payload and a DRD. As also described herein oligomers and polypeptides include one or more payloads and a modulation hub comprising at least two DRDs. The monomers, oligomers, and polypeptides optionally include one or more additional components such as linkers, hinges (e.g., sheddable and non-sheddable hinges), tails (e.g., cytoplasmic tails), and transmembrane domains. As described below in the section related to methods of making, one of skill in the art may select from the various components using guideposts provided below to achieve a desired outcome (e.g., location of the oligomerization domain, payload, or DRD relative the cell in which it is expressed, whether or not the payload is secreted from the cell or tethered to the membrane, or the desired activity of the payload or payloads).
In general, modulation hubs are polypeptides designed to facilitate regulation of a characteristic (e.g., abundance or activity) of a target payload to which it is operably linked and whose foundational building blocks are DRDs. Modulation hubs according to this disclosure comprise at least two DRDs, and in some embodiments such hubs may be formed upon oligomerization of at least two polypeptide monomers as described herein. Thus, in some embodiments, at least two DRDs are linked together via non-covalent bonds formed through oligomerization, optionally by oligomerization domains associated with each DRD as illustrated in
DRDs interact with a ligand such that, when the DRD is operatively linked to a payload, it confers ligand-dependent reversible regulation of a characteristic of the payload (for example, activity). Although referred to as drug responsive domains, the ligand to which a DRD is responsive need not be a drug. Suitable DRDs (and their paired ligands), which may be referred to as destabilizing domains or ligand binding domains, are also known in the art. See, e.g., U.S. Pat. Nos. 9,487,787 and 10,137,180, U.S. Publication Nos.: 2019/0192691; 2020/0101142; 2020/0172879; 2021/0069248, and U.S. patent application Ser. Nos. 17,251,635; and 17/288,373, and WO2018/161000; WO2018/231759; WO2019/241315; U.S. Pat. Nos. 8,173,792; 8,530,636; WO2018/237323; WO2017/181119; US2017/0114346; US2019/0300864; WO2017/156238; Miyazaki et al., J Am Chem Soc, 134:3942 (2012); Banaszynski et al. (2006) Cell 126:995-1004; Stankunas, K. et al. (2003) Mol. Cell 12:1615-1624; Banaszynski et al. (2008) Nat. Med. 14:1123-1127; Iwamoto et al. (2010) Chem. Biol. 17:981-988; Armstrong et al. (2007) Nat. Methods 4:1007-1009; Madeira da Silva et al. (2009) Proc. Natl. Acad. Sci. USA 106:7583-7588; Pruett-Miller et al. (2009) PLOS Genet. 5: e1000376; and Feng et al. (2015) Elife 4: e10606, the contents of each of which are hereby incorporated by reference in their entirety.
Certain of these and other example DRDs suitable for use with modulation hubs according to this disclosure are also provided elsewhere in this specification.
The DRDs, by way of example, can be chosen from FKBP (SEQ ID NO:93), ecDHFR (SEQ ID NO:18), hDHFR (SEQ ID NO:37), ER (SEQ ID NO:96), PDE5 full length (SEQ ID NO:95), PDE5 ligand binding domain (SEQ ID NO:94) and CA2 (SEQ ID NO:1) or a portion of any of the foregoing that maintains DRD function or an amino acid sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identity to SEQ ID NOs: 1, 18, 37, 93, 94, 95, or 96 or the DRD functional portion thereof. One or more mutations (including truncations, substitutions, and deletions) in the amino acid sequence of FKBP, ecDHFR, hDHFR, ER, PDE5, and CA2, for example, can be advantageous to further destabilize the DRD.
Numerous DRD are described herein, but one of skill in the art can identify additional DRDs suitable for use with modulation hubs and in regulatable compositions according to this disclosure. By way of example, DRDs can be identified using library screening and structure-guided engineering to select the optimal DRD variant with sufficient instability in the absence of the ligand and sufficient stability in the presence of the ligand. A variant library can be generated using random mutagenesis screening by transducing cells (e.g., Jurkat cells) with mutant DRD candidates. To produce an enriched library, cells with the desired characteristics (low basal activity/expression and high dynamic range) are selected by testing polypeptide abundance across a range of concentrations of ligand. Single cell clones are then produced and characterized to identify candidate DRDs.
The DRDs described herein are responsive to a paired ligand (also referred to as a “stabilizing ligand” or simply as a “ligand.” Optionally, the DRDs are responsive to a paired ligand that is a small molecule drug, such as an FDA-approved small molecule. However, one of skill in the art can select the DRD and its paired ligand to meet the specific needs of the system. Examples of DRD/ligand pairs are shown in Table 1.
E.
coli dihydrofolate
Optionally, a DRD of the present disclosure may be derived from a carbonic anhydrase, which is a member of a superfamily of metalloenzymes. For example, human carbonic anhydrase (hCA2) can be adapted for use as a DRD. A DRD of the present disclosure may be derived from amino acids 1-260 of CA2 (Uniprot ID: P00918). Optionally, DRDs are derived from CA2 comprising amino acids 2-260 of the parent CA2 sequence (e.g., amino acids 2-260). This is referred to herein as a CA2 M1del mutation (CA2; SEQ ID NO: 5). Optionally, a DRD of the present disclosure comprises a region of or the whole human carbonic anhydrase 2, and further comprises one or more mutations relative to the full-length sequence selected from M1del, L156H, and S56N. Optionally, the DRD is selected from the group consisting of SEQ ID NOs: 1, 3, 5, 7 and 9.
For purposes of this disclosure, oligomerization domains are sequences that promote self-assembly of monomers into oligomers, for example, by non-covalent bonding. Such domains may be found in nature and may be adapted for use in forming oligomers including a payload and modulation hub as described herein. Examples of oligomerization domains include, but are not limited to, phospholamban, collectin, collagen, VASP, CD40L, TNFSF (e.g., TNFSF14, also referred to herein as LIGHT and 4-1BBL), langerin, DAP12, and NKG2C. Optionally, the oligomerization domain is a phospholamban transmembrane domain, collagen 18, avidin, streptavidin, CD40L extra cellular domain (ECD), langerin ECD, 4-1BBL ECD, VASP tetramer, DAP12, LIGHT extracellular domain (ECD), collectin 7, fungal lectin (5xzk), aspartate transcarbomylase (1EKX), 4-OT trimer, RH3 designed coiled coil (1TGG), HIV-1 gp41, FIV dUTP pyrophosphate, SIV gp41, the Ebola virus gp-2, HTLV-1 gp-21 domain, a foldon domain, a GCN4 domain, a T4 fibritin domain, the yeast heat shock transcription factor, and human collagen VIII, Collagen 18, Collagen 15 and hnRNP. Certain oligomerization domains do not oligomerize with themselves and only oligomerize with a different oligomerization domain, such as NKG2C. Such oligomerization domains are referred to herein as hetero-oligomerization domains.
Thus, although the example modulation hubs depicted in
By way of example, the payload can be any polypeptide having a desired biological function. Such payloads can be modified polypeptides such as glycosylated polypeptides or lipopeptides, which upon expression are modified in a cell by constitutive enzymatic activity or by over-expression of selected enzymes. Payloads include multiple classes of therapeutically important polypeptides or any active portion thereof. For example, payloads include Type I/II membrane proteins such as CD40L, 4-1BBL, and CAR or active portions thereof. Payloads also include cytokines such as IL15, IL12, IL1B, IL2, IL7, IL18, IL21, IL23, IL36, TNFα, IFNγ, IFNα, IFNβ, etc., including membrane-tethered forms thereof or active portions thereof. Payloads also include intracellular polypeptides such as dnSHP2, T7, RNA polymerase, Cas9, or active portions thereof. Payloads include secreted proteins such as VEGF-trap, and native cytokines, or active portions thereof. And payloads further include transcription factors such as Foxp3, c-Myc, STAT5, and c-Jun, or active portions thereof, or constitutively active versions thereof. Other examples of suitable payloads include cytokine receptors, T-cell receptors (TCR), chimeric antigen receptors (CAR), immunomodulatory proteins in addition to those already exemplified, or any active portion thereof. The payload can also be a gene editing polypeptide or transcription factor in addition to those previously exemplified. The payload can also be a combination of polypeptides having a desired combination of actions, or active portions thereof.
In some embodiments, payloads are therapeutic agents chosen from a cancer therapeutic agent, a therapeutic agent for an autoimmune disease, an immunotherapeutic agent, an anti-inflammatory agent, an anti-pathogenic agent, a gene therapy agent, or combinations thereof. The immunotherapeutic agent may be an antibody or fragments and variants thereof, a TCR, a CAR, a chimeric switch receptor, an antagonist of a co-inhibitory molecule, an agonist of a co-stimulatory molecule, a cytokine, a mutated version of a cytokine possessing altered receptor binding properties (also called a mutein), a cytokine receptor, a chemokine, a chemokine receptor, a metabolic factor, a coagulation factor, an enzyme, a homing receptor, a kinase, a phosphatase, a dominant negative version of a phosphatase (such as SHP-1 or SHP-2), a dominant negative signaling molecule or receptor (such as a dominant negative Fas Receptor), a dominant negative transcription factor, and a safety switch.
In some embodiments, payloads of the present disclosure may be cytokines, and fragments, variants, analogs and derivatives thereof, including but not limited to interleukins, tumor necrosis factors (TNFs), interferons (IFNs), TGFβ, and chemokines. The interleukins may be chosen from IL15, IL12, IL1β, IL2, IL7, IL18, IL21, IL23, IL36, and variants thereof including membrane-bound, secreted, fusion polypeptide, or cytokine mutants with altered receptor binding properties (such as muteins), and bicistronic forms of the interleukins, and combinations thereof.
For example, IL12 may include both p35 and p40 subunits encoded by a single nucleic acid that produces a single chain polypeptide. The single chain polypeptide may be generated by placing the p35 subunit at the N terminus or the C terminus of the single chain polypeptide. Similarly, the p40 subunit may be at the N terminus or C terminus of the single chain polypeptide. By way of another example, the payload may be a bicistronic IL12 containing p40 and p35 subunits.
In some embodiments, the payload can be an active portion or variant of a polypeptide with a desired biological function, so long as the payload retains the desired biological function. By way of example, the payload may be the p40 subunit of IL12 or the p35 subunit of IL12 or a variant of IL12 that promotes NK cell survival, regulates NK cell and T cell activation and proliferation, and/or supports NK cell development from hematopoietic stem cells.
In some embodiments, payloads of the present disclosure may be chimeric antigen receptors (CARs) comprising an extracellular targeting domain (e.g., a scFv that recognizes a specific tumor antigen or other tumor cell-surface molecules), a transmembrane domain/region, and an intracellular signaling/activation domain (e.g., the signal region of CD3ζ, and/or one or more costimulatory signaling domains, such as those from CD28, 4-1BB (CD137) and OX-40 (CD134)).
In some embodiments, payloads can be selected that reduce immune responses in a subject. For example, the payload can be an anti-cytokine, such as neutralizing antibodies to tumor necrosis factor (TNF)-α or an interleukin. In some embodiments, payloads of the present disclosure target B-cell depletion, such as neutralizing antibodies to CD20, CD22, CD28, CTLA-4, and B-lymphocyte stimulator (BLyS).
In some embodiments, payloads can also be contractile proteins (e.g., actin and myosin), enzymes (e.g., lactase and pepsin), hormones (e.g., insulin, oxytocin, and somatotropin), structural proteins (e.g., keratin, collagen, and elastin), storage proteins (e.g., ovalbumin and ferritin), transport proteins (e.g., hemoglobin), membrane-bound proteins (e.g., class I, II, or III transmembrane proteins; receptors, transporters, and the like).
In some embodiments, payloads of the present disclosure may be one or more components of a gene editing system. In such embodiments, the oligomer or engineered, regulatable polypeptide regulates activity of the gene editing system and consequently expression of a downstream target protein. A target protein, as used herein, refers to a protein selected for gene editing, including, for example, a protein having a genetic mutation that results in a deleterious effect in a subject or in a cell. For example, payloads of the present disclosure may be a Cas protein (CRISPR-associated protein), including Cas9 and Cas12. The Cas protein may be altered or otherwise modified. For example, the Cas protein may be a deadCas9. Optionally, the Cas9 protein is an enzymatically active Cas9 protein, a Cas9 protein wild-type protein, a Cas9 protein nickase or a nuclease null or nuclease deficient Cas9 protein. Such payloads optionally include nucleases (e.g., Zinc finger nuclease, TALEN (Transcription activator-like effector-based nucleases), or meganucleases) and/or recombinases, such as a Cre recombinase.
Payloads useful in the present disclosure also include polypeptides involved in nucleic acid synthesis and replication, for example, DNA and RNA polymerases, transcription factors, primases, helicases, RNases, ligases, topoisomerases, endonucleases, IRES, and telomerases.
Linker sequences (linkers) are known in the art and are described in references cited herein. Linkers include, for example, GS linkers, GSG linkers, and GGSG (SEQ ID NO: 239) linkers. These linkers are repeats of the subunit one or more times. Thus, a GS linker is a GSn linker (SEQ ID NO:240) where n is a numerical number being 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more. Similarly, a GSG linker is a GSGn linker (SEQ ID NO:241) wherein n is a numerical number being 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more. A GGSG linker (SEQ ID NO: 239) is a GGSGn linker (SEQ ID NO:242) where n is a numerical number being 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more.
A hinge sequence is a short sequence of amino acids that facilitates flexibility between connected components. The hinge sequence can be any suitable sequence derived or obtained from any suitable molecule. The hinge sequence may be derived from all or part of an immunoglobulin (e.g., IgG1, IgG2, IgG3, IgG4) hinge region, i.e., the sequence that falls between the CH1 and CH2 domains of an immunoglobulin (e.g., an IgG4 Fc hinge), or the extracellular regions of type 1 membrane proteins such as CD8a CD4, CD28 and CD7, which may be a wild type sequence or a derivative thereof. Some hinge regions include an immunoglobulin CH3 domain or both a CH3 domain and a CH2 domain. In some embodiments, the hinge is derived from a transmembrane domain.
Transmembrane domains, useful in the engineered regulatable polypeptide constructs of the present disclosure can include, for example, a MHC1 transmembrane domain, a CD8α transmembrane domain, a B7-1 transmembrane domain, a CD4 transmembrane domain, a CD28 transmembrane domain, a CTLA-4 transmembrane domain, a PD-1 transmembrane domain, or a human IgG4 Fc region.
Optionally, the herein provided monomers or polypeptide constructs comprise an intracellular/cytoplasmic or transmembrane tail. Optionally, the intracellular/cytoplasmic or transmembrane tail is a CD8, CD40L, LIGHT, NKG2C, or B7.1 intracellular tail. The absence of a transmembrane region in a construct can be, for example, designed for a secreted payload or a payload with intracellular or intranuclear activity.
Optionally, the monomers or polypeptides described herein include a tag. Such a tag allows for isolation or detection of the monomer or polypeptide or for isolation or detection of the payload. Such tags optionally include fluorescent proteins (e.g., green fluorescent protein), His-tag, HA-tag, Myc tag, FLAG tag, mCherry, CD20, CD34, nerve growth factor receptor (NGFR), truncated NGFR (tNGRR), epidermal growth factor (EGFR), or a truncated EGFR (tEGFR).
Ligands may be any agent that binds to the DRDs of the modulation hubs of the engineered, regulatable polypeptides or oligomers described herein, an effective amount of which results in a measurable change in a modification of a characteristic (e.g., abundance, availability, activity) of a payload operably linked to the DRD. In some embodiments, ligands may be synthetic molecules. In some embodiments, stabilizing ligands of the present disclosure may be small molecule compounds. Stabilizing ligands are optionally small molecule therapeutic drugs previously approved by a regulatory agency, such as the U.S. Food and Drug Administration (FDA). Examples of stabilizing ligands and their corresponding DRDs suitable for use in the modulation hubs described herein are shown in Table 1, in patents and applications referenced above in the section exemplifying suitable DRDs, and in U.S. Pat. No. 9,487,787 filed Mar. 33, 2012, U.S. Pat. No. 10,137,180 filed Sep. 6, 2013, PCT Application No. PCT/US2018/037005, filed Jun. 12, 2018, PCT Application No. PCT/US2019/036654 filed Jun. 12, 2019, PCT Application No. PCT/US2019/057698 filed Oct. 23, 2019, PCT Application No. PCT/US2020/021596 filed Mar. 6, 2020, and U.S. application Ser. No. 16/558,224 filed Sep. 2, 2019, the disclosures of all of the aforereferenced applications are incorporated herein by reference in their entireties.
Provided herein are expressible nucleic acid constructs encoding one or more engineered, regulatable polypeptide monomers or regulatable polypeptides as described herein. In embodiments, the nucleic acid constructs encoding a monomer include an oligomerization domain and at least one DRD and/or at least one payload and optionally comprise additional components, such as hinges, linkers, transmembrane domains, tags, and intracellular/cytoplasmic and transmembrane tails as described herein. In certain embodiments, a single nucleic acid construct comprises nucleic acid sequences that encode all components of a monomer as described herein. For example, the nucleic acid construct encodes at least a payload, a DRD, and an oligomerization domain. When expressed multiple times, the monomers can assemble into oligomers, for example, dimers, trimers, tetramers, pentamers or hexamers depending on the oligomerization domain and by way of the oligomerization domain. Optionally, a single nucleic acid construct encodes multiple copies of the same or different monomers, which, when expressed assemble into an oligomer. Optionally, certain nucleic acid constructs encode an oligomerization domain and at least one payload, and certain nucleic acid constructs encode an oligomerization domain and at least one DRD, such that when expressed they assemble into an oligomer comprising at least one payload and at least two DRDs.
In embodiments, the nucleic acid constructs encoding regulatable polypeptides include at least one payload and at least one modulation hub comprising at least two DRDs. The nucleic acid constructs encoding regulatable polypeptides may include additional components such as hinges, linkers, transmembrane domains, tags, and intracellular/cytoplasmic and transmembrane tails as described herein.
The nucleic acid constructs encoding monomers and regulatable polypeptides optionally also encode additional components such as signal sequences and cleavage sites including shedding domains. The constructs optionally further comprise a promoter sequence and other regulatory elements (enhancers, translational control elements (e.g., IRES), and elements that control half-life).
Further provided is a plurality of nucleic acid constructs, each construct encoding one or more monomers or polypeptides described herein. Such a plurality of constructs, upon expression, optionally provide for monomers that oligomerize. The constructs of the plurality can be the same or different. Thus, the nucleic acids of the plurality may encode the same polypeptides or monomers or may encode polypeptides or monomers comprising different DRDs, payloads, and/or additional components.
Also provided herein are vectors for expressing one or more of the nucleic acids. Such a vector can be chosen from viral vectors and non-viral vectors, plasmids, cosmids, and artificial chromosomes. By way of example, the vector can be a viral vector, such as a lentiviral vector, a retroviral vector, an adenoviral vector, or an adeno-associated viral vector. The vector optionally comprises nucleic acid sequences that encode transposases and/or nucleases. Non-viral vector examples include physical vectors such as electroporation and chemical vectors such as lipid nanoparticles.
Cells containing one or more nucleic acid constructs or vectors as described herein are provided. The cell provides an expression system or a therapeutic target for the monomers, oligomers, or polypeptides described herein. Suitable cells include immune cells or stem cells. Optionally, the immune cells are primary human T cells, such as T cells derived from human peripheral blood mononuclear cells (PBMC), PBMC collected after stimulation with G-CSF, bone marrow, or umbilical cord blood. In embodiments, the immune cells are tumor infiltrating lymphocytes (TILs), for example collected from a tumor. The immune effector cells may also be NK cells, αβ Tcells, iNKT cells, γδT cells, macrophages, B cells, dendritic cells, myeloid derived progenitor cells, eosinophils, basophils, neutrophils, or Tregs. Optionally, the stem cells are hematopoietic stem cells, human embryonic stem cells, or iPSCs. The cells provided herein are optionally mammalian cells, or, more specifically, human cells.
The present disclosure provides methods of making nucleic acid constructs and vectors encoding monomers and polypeptides of this disclosure, methods of making the monomers and polypeptides of this disclosure by expression of nucleic acid constructs, and methods of making cells comprising the nucleic acid constructs or vectors described herein.
As another example, linker and linker length may influence “constitutive” activity level (i.e., basal activity in the absence of ligand) and in embodiments, the specific linker and length is chosen to maximize the on state (e.g., maximum activity level) while maintaining low basal activity level and ligand (e.g., drug) responsiveness. As yet another example, the specific hinge may allow for conformational changes and thereby influence ligand responsiveness and is thus chosen to result in a sufficient dynamic range to obtain a desired range of payload abundance and biologic activity (i.e., an acceptable payload activity range that corresponds to variation in ligand from zero or minimal to maximum saturation). By way of example, as shown in
In some embodiments, the nucleic acid sequences encoding polypeptides or monomers may be engineered to include one or more additional components, such that, when expressed in a cell, result in the payload localizing internal to the cell membrane (optionally, tethered to the membrane or released into the cytoplasm) and, in certain embodiments, external to the cell membrane (optionally, tethered to the membrane or released extracellularly (i.e., shed or cleaved off of the membrane). Similarly, the nucleic acid constructs are optionally configured to encode polypeptide monomers that oligomerize by way of association of an intracellular, transmembrane, or extracellular oligomerization domain. Thus, all or a portion of the modulation hub or oligomerization domain can be engineered to reside intracellularly, within the cell membrane, or on the surface of the cell (e.g., tethered to the cell surface). See
In some embodiments, the nucleic acid sequences encoding polypeptide monomer constructs or regulatable payload compositions may be engineered to include one or more of these additional components such that, when expressed in a cell, the regulatable payload composition is engineered with a signal sequence to transport part or all of the engineered regulatable polypeptide construct into the secretory pathway.
After designing the construct for proper function including localization, appropriate components such as promoters, enhancers, multicistronic expression, translation control and half-life control elements are selected to achieve the desired control of payload abundance or activity. Additionally, nucleic acid constructs are designed for cistronic or multicistronic expression as required for the desired expression of various engineered components.
Additionally, vehicles/vectors are chosen and designed to deliver the nucleic acid constructs into the desired cell. For example, the vehicles may be chosen from those previously described including viral vectors (such as lentiviral vectors, retroviral vectors, and adeno-associated vectors), plasmids, cosmids, and artificial chromosomes. Such vectors can be designed to encode transposases, nucleases, and elements that control translation (e.g., IRES). The choice of vector may also influence the choice of various building block components. For example, vectors which demand smaller constructs may require using smaller DRDs.
Cells for engineering can be isolated from any biological sample, including for example, blood (e.g., umbilical cord blood or peripheral blood), bone marrow, fetal tissue (human embryonic stem cells), or tumors. Cells can be modified cells, such as a stem cell modified to be pluripotent (e.g., an induced pluripotent stem cell (iPSC)) or CAR T cells, prior to transduction with the described nucleic acids and vectors.
By way of example, isolated T cells or tumor infiltrating lymphocytes (TILs) can be isolated from a biological sample, transduced, and, optionally, expanded in culture. Such expansion can be performed, for example, by contacting the transduced cell with IL2, feeder cells, recombinant antigen, or an antibody that stimulates cell expansion.
The cell to which the nucleic acid is delivered is selected based, at least in part, on the ability of the cell to allow expression of the polypeptides or monomers disclosed herein and to allow payload activity in a sufficient dynamic range. Optionally, the cell expresses little or no payload in the absence of the provided nucleic acid or vector. In certain embodiments, one of skill in the art would select a cell in need of an increase in payload activity or abundance in a cell that expresses the payload. In certain embodiments, one of skill in the art would select a cell in need of gene editing. In certain embodiments the cell is selected as an effector cell, for example, an immune effector cell.
A person of ordinary skill in the art applying knowledge from this disclosure can build a variety of monomers, polypeptides, and oligomers, as well as nucleic acids and vectors encoding them within scope of this disclosure beyond those explicitly exemplified herein. For example as described, modulation hubs, payloads, DRDs, oligomerization domains, and additional components such as linkers, tails, transmembrane domains, signal sequences, hinges, and the like can be selected to create a variety of polypeptides, oligomers, and nucleic acids encoding them upon considering such factors as desired therapeutic outcome, whether the payload is membrane-bound or secreted, whether the payload acts intracellularly or extracellularly, and whether the oligomerization domain should be located intracellularly, extracellularly, or transmembrane. Accordingly, the example embodiments are non-limiting and help provide guidance for a person of skill in the art to implement other embodiments within the scope of this disclosure.
Disclosed herein are methods of regulating payload function, for example methods of regulating abundance, availability and/or activity (“activity”) of a payload. In some embodiments, the method of regulation is a method of modifying the activity of the payload comprising engineering a cell to express a payload operably linked to a modulation hub comprising two or more DRDs responsive to a ligand. In some such embodiments, the activity of the payload (e.g., corresponding to the abundance and/or availability of the payload) is reduced as compared to the activity of a payload in a control cell, for example, a cell engineered to express the payload independent of a DRD.
Optionally, the payload has a biological activity level ranging from a basal activity level in the absence of ligand to a maximum activity in the presence of a saturating amount of ligand, and the method is a method of modulating the activity of a payload comprising contacting a cell engineered to express a payload operably linked to a modulation hub with an effective amount of ligand such that the activity of the payload is increased relative to the basal activity level. In some embodiments, the method comprises contacting the cell with a selected amount of ligand, wherein the selected amount of ligand results in a selected activity level of the payload. In certain embodiments, the method comprises alternatively contacting the cell with varying selected amounts of ligand, to achieve varying selected activity levels ranging from the basal level to the maximum level.
The contacting step can occur in vitro, ex vivo, or in vitro. The contacting step is optionally performed to achieve a continuous selected activity of the payload (i.e., to achieve a continuous on-state of the payload) or to achieve intermittent activity of the payload (i.e., to provide a pulsed delivery of the payload between an on-state and an off-state). “Off-state” means the payload activity is the basal activity level. “On-state” means a selected activity level in the presence of an effective amount of ligand, which is greater than the off-state. Continuous activity of the payload can be achieved by continuous contact of the DRDs with an effective amount of ligand or by providing a subsequent contacting step or steps of the DRDs with the ligand, wherein the subsequent contacting step or steps is/are performed before the activity level of the payload from the previous contacting step reaches the basal activity level. Each contacting step can be varied with regard to the amount of ligand such that, when more ligand is used, more payload activity results, and, when less ligand is used, less payload activity results. Thus, the amount of ligand can be varied with subsequent contacting steps to tune up or tune down the amount and/or activity of the payload over time. Each contacting step can also be varied with respect to frequency in order to achieve a desired pattern of activity level. Because the modulation hubs as described herein result in a lower off-state and optionally a wider dynamic range of activity for a payload as compared to the same payload in a control construct, the activity of the payload can be regulated from a lower off-state and optionally varied over a greater range as compared to a payload in a control construct.
Also disclosed are methods of delivering a payload to a subject, for example a therapeutically effective payload to a subject in need thereof, whereby a nucleic acid construct or a vector as described herein is administered to the subject. The method results in expression, for example in target cells of the subject, of one or more polypeptides or monomers, which monomers self-assemble to form oligomers as described herein. The methods may further comprise controlling the dose or duration of administration of a payload to a subject. For example, the method optionally further comprises administering to the subject a selected amount of paired ligand to deliver a selected activity of the payload to the subject. The ligand can be delivered to achieve continuous or intermittent payload activity in the subject. Continuous payload activity may be a substantially consistent level of activity, or the level of activity may be modulated. Intermittent activity, between the off-state and on-state includes modulating activity between the off-state and a substantially consistent on-state, or between the off-state and varying on-state activity levels. A higher dose or longer duration of administration of the ligand is administered when more activity of the payload is desired, and reduction or elimination of the ligand dose is chosen when less activity is desired. The dose and duration of ligand administration and the resulting activity of the payload may be selected to avoid unacceptable or undesired side effects or toxicity in the subject. Dosages of ligand and schedules for administering the dosages of ligand may be determined empirically by one skilled in the art based on the amount of resulting payload, the activity of the payload, or based on one or more signs of the effect of the payload activity. The ranges for administration of the ligand range from any amount above zero to a saturating dose and the resulting payload activity ranges from a basal level to a maximal level, optionally with a sufficient dynamic range that allows for the desired dose-response to the ligand and concomitant activity range for the payload (e.g., for a given ligand and payload, the range of difference in off-state and maximum payload activity would result from at least a 10 fold range of ligand). This sufficient dynamic range allows for fine tuning and a dose response curve that is not unacceptably steep. In embodiments, the dosage or frequency of administration of ligand and resulting abundance and activity of payload is chosen to avoid, mitigate against, or limit unacceptable or undesired adverse side effects and will vary with the age, condition, and/or sex of the subject, and type of condition being treated, the extent of the condition, or, and whether other therapeutic agents are included in the treatment regimen. Guidance can be found in the literature for appropriate dosages for given classes of ligands.
By way of further example, for a subject with cancer, a nucleic acid construct or vector according to this disclosure is provided to a subject, wherein the nucleic acid construct or vector encodes a payload operably linked to a modulation hub and wherein the payload targets a tumor cell or an immune cell that in turn targets the tumor cell. Such a method optionally comprises administering to the subject a nucleic acid construct or vector according to this disclosure encoding a payload operably linked to a modulation hub, wherein the payload is an immune checkpoint inhibitor, a cytokine, CAR, or TCR.
Also provided herein are methods of delivering a payload operably linked to a modulation hub to a subject by administering to the subject a cell containing a nucleic acid or vector described herein. Such a method can further comprise isolating cells from a subject, transducing the isolated cells with the nucleic acids or vectors encoding the monomers (which when expressed assemble into regulatable oligomers) or regulatable polypeptides described in this disclosure, expanding the cells in vitro, and providing the cells to the same or different subject. The payload is selected to treat the subject receiving the cells. The subject may have cancer, an autoimmune disease, a genetic mutation, a deficiency in an essential polypeptide or the like. The transduced cells can be, by way of example, immune effector cell (e.g., an NK cell, iNKT, αβ T cell, γδ T cell, tumor infiltrating lymphocyte (TILs), macrophages, B cells), or stem cells). The cells can be isolated from the same subject (autologous source) that receives the transduced cells or the cells can be isolated from a different subject (e.g., an allogeneic source). By way of example, when the subject has cancer, a T cell or TIL can be isolated from the subject and engineered to express a cytokine, a CAR, and/or a TCR. For example, the cell can be a CD19 CAR-T cell. The cell is optionally expanded, and the cell or the expanded population of cells is administered to the same or different subject. In certain embodiments, the T-cells, CAR-T cells, NK cells, or TILs, are administered in an amount from about 1000 cells/injection to up to about 10 billion cells/injection, such as 1×1010, 1×109, 1×108, 1×107, 5×107, 1×106, 5×106, 1×105, 5×105, 1×104, 5×104, 1×103, 5×103 cells per injection, or any ranges between any two of the numbers, end points inclusive. Optionally, from 1×108 to 1×1010 cells are administered to the subject. Optionally, the cells are administered one, two, three, or four times as needed.
In the treatment methods, the ligand dosage regimen including the selected amount of ligand for administration to the subject and frequency of administration of the selected amount of ligand is chosen to result in regulation of the payload and/or a desired outcome for the subject. The subject is optionally monitored for the outcome. Thus, for example, the number of malignant cells in a sample, the circulating tumor DNA in a sample, or the size of a solid tumor upon imaging can be detected. If the desired end point is achieved (e.g., showing successful treatment of cancer), the ligand can be reduced or discontinued so as to reduce or eliminate the payload, for example to reduce the abundance, availability and/or activity of the payload below a pre-determined threshold to eliminate or mitigate against unwanted or undesired side effects. Similarly, if the subject develops a cytokine storm, an allergic reaction, or other adverse effect from the payload, the ligand can be reduced or discontinued. Also disclosed herein are methods of regulating expression of a downstream target protein of a gene editing process. In some embodiments, such method comprises engineering a cell to express an oligomer or engineered, regulatable polypeptide comprising a payload such as a CAS9 protein or transcription factor protein operably linked to a modulation hub. In certain embodiments, for a subject with a genetic mutation, a nucleic acid construct or vector according to this disclosure is provided to deliver a payload that provides a nucleic acid editing polypeptide or system operably linked to a modulating hub. Target cells in the subject are transduced with the nucleic acid construct or vector to allow the gene editing payload to modify the nucleic acid (e.g., genomic DNA or RNA) of the transduced cell. The activity level of the payload and therefore expression of the target protein can be regulated by administration of ligand to the subject. Systems for nucleic acid editing are known in the art, such as CRISPR/Cas 9 systems, TALENs, retrotransposons, and the like. The nucleic acid construct or vector can be engineered to encode one or more components of any one of the systems, such that one or more nucleic acids in the transduced cell of the subject is edited to provide a desired nucleic acid modification.
The terms “about” and “approximate,” when used to refer to a measurable value such as an amount, concentration, dose, time, temperature, activity, level, number, frequency, percentage, dimension, size, weight, position, length and the like, is meant to account for variations due to experimental error, which could encompass variations of ±15%, ±10%, ±5%, ±1%, ±0.5%, or even ±0.1% of the specified amount, concentration, dose, time, temperature, activity, level, number, frequency, percentage, dimension, size, weight, position, length and the like. All measurements or numbers are implicitly understood to be modified by the word about, even if the measurement or number is not explicitly modified by the word about. In instances in which the terms “about” and “approximate” are used in connection with the location or position of regions within a reference polypeptide, these terms encompass variations of ±up to 20 amino acid residues, ±up to 15 amino acid residues, ±up to 10 amino acid residues, ±up to 5 amino acid residues, ±up to 4 amino acid residues, ±up to 3 amino acid residues, ±up to 2 amino acid residues, or even ±1 amino acid residue.
Reference is made herein to a “basal activity level.” Basal level as used herein can be zero, near zero, or any amount in the absence of exogenous ligand. Basal activity may occur because of endogenous levels of the same or different ligand or may occur because of a resting level of payload production in the absence of exogenous ligand.
Reference to “biological activity” is understood to mean under appropriate conditions even if not so stated.
As used herein “contacting” is understood to mean providing an agent (such as a ligand) to a target (such as a DRD) such that the agent and target may come into contact with one another. For example, contacting includes providing a ligand in vitro to a cell (e.g. when the DRD is located extracellularly or on the cell surface). As another example, contacting also includes providing the ligand to a cell, wherein the DRD is located intracellularly, such that the ligand reaches the cytoplasm. Similarly, a cell can be contacted in vivo, by administering a ligand to a subject such that the ligand reaches a cell or DRD.
As used herein, the term “control construct” refers to a construct similar to the test engineered, regulatable oligomer or engineered regulatable polypeptide (“test construct”) except the control construct lacks an oligomerization domain and has only a single DRD.
“DRD” is understood to mean a domain responsive to a ligand, even if not so stated.
A “hetero-oligomerization domain” as described herein is a first oligomerization domain on a first monomer that promotes oligomerization through a second oligomerization domain on a second monomer, wherein the second oligomerization domain is different than the first and wherein the first oligomerization domain does not promote oligomerization with an oligomerization domain that is the same.
The terms “ligand,” “paired ligand,” and “stabilizing ligand” are used interchangeably and mean the same thing when used in reference to a drug responsive domain (“DRD”) and/or modulation hub.
As used herein, “operably linked” means that, in the presence of a paired ligand, the modulation hub or DRD is linked to the payload directly or indirectly so as to alter a measurable characteristic of the payload (e.g., alters the level of activity of the payload as compared to the level of activity in the absence of the paired ligand). In some embodiments, the measured level of amount and/or activity of the payload increases in the presence of an effective amount of ligand as compared to the measured level of expression or activity in the absence of ligand. An effective amount of ligand means the amount of ligand needed to see an increase in the measure of the amount or activity of the payload. In some embodiments, the effective amount is not so great as to produce unacceptable toxicity or off-target effects. Optionally, the measurable characteristic is a therapeutic outcome, an amount of the payload in a sample, or a biological activity level of the payload (for which measuring the amount of payload can serve as a proxy).
The term “payload” refers to the agent whose abundance, activity, availability, expression, function or other characteristic is desired to be regulated by a DRD and/or modulation hub.
Wherever the phrase “linked” or “bound” or the like is used, the phrase “directly or indirectly” is understood to follow unless explicitly stated otherwise or nonsensical in context. Thus, the phrase “a DRD linked to another DRD” or “two linked DRDs” means in both cases that a first DRD is directly or indirectly linked to a second DRD. For example, “two linked DRDs” and the like covers the situation wherein two DRDs are not directly connected to one another but rather are in association with one another because each is connected to an oligomerization domain, and the respective oligomerization domains are linked, e.g., via non-covalent bonds.
The details of one or more embodiments of the present disclosure are set forth in the description and accompanying drawings. It is to be understood that other embodiments may be utilized and structural or process changes made without departing from the scope of the disclosure. In other words, illustrative embodiments and aspects are described below. But it will be appreciated that in the development of any such actual embodiment, numerous implementation-specific decisions may be made to achieve the developer's specific goals, such as compliance with system-related and business-related constraints, which may vary from one implementation to another. Moreover, it will be appreciated that such development effort might be complex and time-consuming but would nevertheless be a routine undertaking for those of ordinary skill in the art having the benefit of this disclosure.
Publications cited herein and the material for which they are cited are hereby specifically incorporated by reference in their entireties.
The examples below are intended to further illustrate certain aspects of the methods and compositions described herein and are not intended to limit the scope of the claims.
IL12-(241-252 and 254-262) and CD19-IL12-(297-316, 319-332) plasmids were each constructed in a pELNS vector (a third-generation self-inactivating lentiviral expression vector) using standard molecular biology techniques. Gene fragments (Gblocks or strings DNA) encoding IL12, Glycine-serine linkers, various hinges, transmembrane domains and cytoplasmic tails were purchased from Integrated DNA Technologies or Thermo-fisher scientific. The gene fragments were inserted into the pELNS vector and placed under the control of the EF1a promoter using Gibson assembly (NEBuilder Hifi). The assembled plasmid was transformed into E. coli (NEB stable) for amplification and sequence confirmed before proceeding with virus production.
HEK-293 and T cells were cultured in standard media (DMEM (Fisher Scientific Cat #11-960-044) with 10% FBS (Fisher Scientific Cat #10-082-147) and 1% P/S (ThermoFisher Cat #15140122). HEK293 and T cells were transiently transfected using manufacturer's protocol with Lipofectamine 2000 and 1 μg plasmid DNA each of: IL12-223, 241, 243, 244, 245, 247, 248, 249, 250, 251, 254, 255, 256, 258 and 260. 100 μM acetazolamide was added one day after transfection, and the cells were further cultured for 1 more day. mCherry was used as a transfection marker and anti-IL12p40/70-V450 Cat #561380 BD was used to stain for IL12. The flow cytometry graphs in
Jurkat, Clone E6-1, cells were cultured in standard media (RPMI+ GlutaMAX Supplement: Life Technologies Cat #61870127, Fetal Bovine Serum (FBS) Life Technologies Cat #10-082-147). Jurkat cells were transduced with lentivirus produced with each of IL12-217, -241, -243, -245, -247, -248, -254, -256, and -258. The components of these constructs are depicted in
On day 0, primary human T cells were stimulated with Dynabeads (T-expander CD3/CD28) at a 3:1 bead:cell ratio in media containing 10% fetal bovine serum (FBS). The next day, lentivirus produced with constructs (IL12-241, 245, 247, 256, 223, 260 and CD19-IL12-192) and controls were added in the presence of reduced serum (5% FBS). The components of these constructs are depicted in
On day 0, primary human T cells were stimulated with Dynabeads (T-expander CD3/CD28) at a 3:1 bead:cell ratio in media containing 10% fetal bovine serum (FBS). The next day, lentivirus produced with constructs expressing mCherry and membrane-bound trimerizing flexi-IL12 (IL12-241, 245, 247, 256, 260, and CD19-IL12-192) and controls were added in the presence of reduced serum (5% FBS). On day 2, the cells were diluted 1:2 with fresh 10% FBS media. On day 5, the cells were analyzed for mCherry transduction media was replaced and cells were treated with 100 μM acetazolamide or DMSO. Twenty-four hours later T cells were analyzed by FACs. mCherry was used as a transduction marker and anti-IL12p40/70-V450 Cat #561380 BD was used to stain for IL12. Alternatively, cells were expanded for a total of 10-11 days and then frozen in liquid nitrogen. Next, T cells were thawed and counted. 1-2×105 cells were plated per well of a 96-well V-bottom plate, re-stimulated with soluble CD3/CD28 Immunocult reagent (Stem Cell Technologies) and treated with a dose response of acetazolamide ranging from 0-100 μM. After overnight incubation, transduction efficiency was analyzed by flow cytometry using mCherry. Surface expressed IL12 was detected with an anti-IL12p70 antibody (BD).
See
On day 2, the cells were diluted 1:2 with fresh 10% FBS media. On day 3 the cells were expanded 1:3 into with fresh medium. On day 6, the cells were assessed for transduction efficiency using flow cytometry. As a readout of cell transduction, CD19-CAR expression was detected using a CD19-Fc reagent followed by a fluorescently labeled anti-human Fc antibody. The Dynabeads were removed using magnetic selection and the cells split 1:2 into fresh medium. On day 8, a normalized number of transduced (CAR+) cells were plated on a 96-well plate and treated with either 20 μM ACZ or an equivalent volume of DMSO vehicle control in the absence or presence of antigen re-stimulation. Stimulation conditions were either human Immunocult soluble CD3/CD28 reagent (StemCell Technologies, catalogue number 10971), K562 cells stably expressing the CAR antigen CD19 at a E:T ratio of 1:1, or parental control K562 cells. After overnight incubation, mbIL12 abundance on transduced T-cells was analyzed by flow cytometry using CD19-Fc followed by a fluorescently labeled anti-human Fc antibody to detect surface CAR expression, anti-IL12p70, anti-CD45, anti-CD3, anti-CD4, and anti-CD8 antibodies. The geometric mean fluorescent intensities (GMFIs) of IL12p70 in transduced cells were normalized against the gMFIs of mbIL12 from identically treated (ligand+antigen restimulation) untransduced cells with values close to 1 reflecting an undetectable amount of mbIL12. Table 4 shows the fold-change of mbIL12 within a restimulation condition was calculated as the gMFI of mbIL12 with ligand added divided by the gMFI without ligand for a given construct.
Cytokine that accumulated in the overnight culture supernatants from 40,000 transduced cells (CD19-CAR+) per 200 μL media were measured using human IL12p70 and/or human interferon-gamma MSD V-plex assay kits (Meso Scale Discovery). Fold-change of IL12 within a restimulation condition was calculated as the concentration of IL12 with ligand added divided by the concentration without ligand for a given construct. All constructs transduced and expanded efficiently in primary human T-cells.
HEK-293T cells are cultured in standard media (DMEM (Fisher Scientific Cat #11-960-044) with 10% FBS (Fisher Scientific Cat #10-082-147) and 1% penicillin/streptomycin (P/S, ThermoFisher Cat #15140122). HEK293T cells are transiently transfected using manufacturer's protocol with Lipofectamine 2000 and 1 μg plasmid DNA each of FOXP3-X constructs (wherein X is varied) as shown in
Multiple TNFSF cytoplasmic tail-TM-hinge combinations (from TWEAK, TRAIL, BAFF, GITRL and APRIL) trimerized using collectin 7 trimerizing domain are used to fine tune regulation of IL12. HEK-293T cells are cultured in standard medium (DMEM (Fisher Scientific, Cat #11-960-044) with 10% FBS (Fisher Scientific, Cat #10-082-147) and 1% P/S (ThermoFisher Cat #15140122). HEK293T cells are transiently transfected using manufacturer's protocol with Lipofectamine 2000 and 1 μg plasmid DNA each of IL12-X (wherein X is varied) as shown in
HEK-293T cells are cultured in standard media (DMEM FisherScientific Cat #11-960-044) with 10% FBS (FisherScientific Cat #10-082-147) and 1%
P/S (ThermoFisher Cat #15140122). HEK293T cells are transiently transfected using manufacturer's protocol with Lipofectamine 2000 and 1 μg plasmid DNA each of FOXP3-X (where X is varied) as shown in
HEK-293T cells are cultured in standard media (DMEM (Fisher Scientific, Cat #11-960-044) with 10% FBS (Fisher Scientific, Cat #10-082-147) and 1% P/S (ThermoFisher Cat #15140122). HEK293T cells are transiently transfected using the manufacturer's protocol with Lipofectamine 2000 and 1 μg plasmid DNA each of IL12-X (wherein X is varied) as shown in
In a similar experiment, HEK-293T cells are cultured in standard media (DMEM (Fisher Scientific, Cat #11-960-044) with 10% FBS (Fisher Scientific, Cat #10-082-147) and 1% P/S (ThermoFisher Cat #15140122). HEK293T cells are transiently transfected using the manufacturer's protocol with Lipofectamine 2000 and 1 μg plasmid DNA each of IL2-X (wherein X is varied) as shown in
HEK-293T cells are cultured in standard media (DMEM (Fisher Scientific, Cat #11-960-044) with 10% FBS (Fisher Scientific, Cat #10-082-147) and 1% P/S (ThermoFisher Cat #15140122). HEK293T cells are transiently transfected using manufacturer's protocol with Lipofectamine 2000 and 1 μg plasmid DNA each of IL2-X (wherein X is varied. 100 μM acetazolamide are added one day after transfection, and the cells are further cultured for 1 more day. mCherry is used as a transfection marker and anti-IL2 antibody (Biolegend Cat #500311) is used to stain for IL2.
HEK-293T cells are cultured in standard media (DMEM (V Cat #11-960-044) with 10% FBS (V Cat #10-082-147) and 1% P/S (ThermoFisher Cat #15140122). HEK293T cells are transiently transfected using manufacturer's protocol with Lipofectamine 2000 and 1 μg plasmid DNA each of IL15-X (wherein X is varied). 100 μM acetazolamide are added one day after transfection, and the cells are further cultured for 1 more day. mCherry is used as a transfection marker and IL15Ra-Fc-biotin (Cat #ILA-82F4 Acrobiosystems) followed by Streptavidin BV421 (Biolegend, Cat #405225) to stain for IL15.
Jurkat cells were transduced to 10-15% positive as determined by using RQR8 as a transduction marker with lentivirus generated using constructs IL12-266, 267 and 268 shown in
On day 0, primary human T cells were stimulated with Dynabeads (T-expander CD3/CD28) at a 3:1 bead:cell ratio in media containing 10% fetal bovine serum (FBS). The next day, lentivirus produced with constructs expressing CD19 CAR and membrane-bound oligomerizing flexi-IL23 (CD19-IL23-002, CD19-IL23-003, CD19-IL23-004, CD19-IL23-005, CD19-IL23-006, CD19-IL23-007, CD19-IL23-008) and control constructs (CD19-IL23-001, which expresses secreted flexi-IL23; CD19-IL23-009, which expresses flexi-IL23 without any oligomerizing modulation hub) were added in the presence of reduced serum (5% FBS). On day 2, the cells were diluted 1:2 with fresh 10% FBS media. On day 5, the cells were analyzed for CD19 CAR expression using CD19-Fc (R&D Systems, Minneapolis, MN; Part #9269-CD-050) followed by anti-human Alexa 647 anti-Human IgG (Jackson ImmunoResearch, West Grove, PA; Part #109-607-003). Media was replaced and cells were treated with 100 μM acetazolamide or DMSO. Twenty-four hours later T cells were analyzed by FACs. CD19 CAR was used as a transduction marker and anti-IL12/IL23p40-PE (Biolegend, San Diego, CA; Cat #501807) was used to stain for IL23 expression. The Geometric MFI of surface IL23p40 expression on CAR+ cells was plotted using Prism Software. The results are shown in
The following constructs were used in this example:
On day 0, primary human T cells were stimulated with Dynabeads (T-expander CD3/CD28) at a 3:1 bead:cell ratio in media containing 10% fetal bovine serum (FBS). The next day, lentivirus produced with constructs expressing CD19 CAR and membrane-bound oligomerizing IFNα (CD19-IFNα-002, CD19-IFNα-003, CD19-IFNα-004, CD19-IFNα-005, CD19-IFNα-006, CD19-IFNα-007, CD19-IFNα-008), and control constructs (CD19-IFNα-001, which expresses secreted IFNα; CD19-IFNα-009, which expresses monomeric IFNα without any oligomerizing modulation hub) were added in the presence of reduced serum (5% FBS). On day 2, the cells were diluted 1:2 with fresh 10% FBS media. On day 5, the cells were analyzed for CD19 CAR expression using CD19-Fc (R&D Systems; Part #9269-CD-050) followed by anti-human Alexa 647 anti-Human IgG (Jackson ImmunoResearch; Part #109-607-003). Media was replaced and cells were treated with 100 μM acetazolamide or DMSO. Twenty-four hours later T cells were analyzed by FACs. CD19 CAR was used as a transduction marker and anti-IFNα PE (BD Biosciences; Cat #560097) was used to stain for IFNα expression. The Geometric MFI of surface IFNα expression on CAR+ cells was plotted using Prism Software. The results are shown in
The following constructs were used in this example:
Jurkat, Clone E6-1, cells were cultured in standard media (RPMI+ GlutaMAX Supplement (Life Technologies; Cat #61870127), Fetal Bovine Serum (FBS) (Life Technologies; Cat #10-082-147)). Jurkat cells were transduced with lentivirus produced with each of CD19CAR-IL2-001, CD19CAR-IL2-002, CD19CAR-IL2-003, CD19CAR-IL2-004, CD19CAR-IL2-005, CD19CAR-IL2-006, CD19CAR-IL2-007, CD19CAR-IL2-008 and IL2-017. Jurkat cells were transduced to 10-25% positive as determined by using CD19 CAR as a transduction marker. CD19 CAR expression was assayed using CD19-Fc (R&D Systems; Part #9269-CD-050) followed by anti-human Alexa 647 anti-Human IgG (Jackson ImmunoResearch; Part #109-607-003). Five days post transduction, the cells were treated with 100 μM acetazolamide or DMSO, and the cells were further cultured for 1 more day. PE Anti-human IL2 antibody (Biolegend; Cat #500307) was used to stain for IL2 expression.
The following constructs were used in this example:
On day 1, primary human T cells were stimulated with Dynabeads (T-expander CD3/CD28) at a 3:1 bead:cell ratio in media containing 10% fetal bovine serum (FBS). The next day, lentiviral vectors were used to transduce the T cells with IL18 oligomerizing constructs. On day 3, the cells were diluted 1:2 with fresh 10% FBS media. On day 4, cells were split 1:4 with fresh 10% FBS media.
On day 6, cells were de-beaded and re-plated at 1×106 cells/mL. The next day cells were left unstimulated or activated with soluble CD3/CD28 (StemCell Technologies) and were treated with either 50 μM acetazolamide (ACZ) or DMSO. After 24 hours, anti-IL18 (Clone 159-12B, MBL Int Cat #D045-3) and anti-Rat IgG2a PE-conjugated Biolegend, Cat #407508) was used to detect membrane-bound IL18 by flow cytometry. Cytokines that had accumulated for 24 hours in the culture supernatants (from 200,000 cells per 200 μL media) were measured using human IL18 MSD V-plex assay kits (Meso Scale Discovery).
On day 1, primary human T cells were stimulated with Dynabeads (T-expander CD3/CD28) at a 3:1 bead:cell ratio in medium containing 10% fetal bovine serum (FBS). The next day, lentiviral vectors were used to transduce the T cells with IL18 oligomerizing constructs. On day 3, the cells were diluted 1:2 with fresh 10% FBS medium. On day 4, cells were split 1:4 with fresh 10% FBS medium.
On day 6, cells were de-beaded and re-plated at 1×106 cells/mL and rested for 48 hours. On day 8, cells were re-plated at 200,000 cells per 200 μL medium and treated or untreated with recombinant 20 ng/ml of human IL15 (Biolegend, Cat #570304). Interferon (IFN)-γ and IL18 that had accumulated for 48 hours in the culture supernatants was measured using customized human IFNγ/IL18 MSD V-plex assay kits (Meso Scale Discovery).
Jurkat, Clone E6-1, cells (ATCC) were cultured in standard media (RPMI+ GlutaMAX Supplement: Life Technologies Cat #61870036, Fetal Bovine Serum (FBS) Life Technologies Cat #A38400-01). Jurkat cells were transduced with lentiviral vectors containing IL18 oligomerizing constructs. Five days post transduction, the cells were treated with 50 μM acetazolamide or DMSO, and the cells were further cultured for 1 more day. Anti-IL18 (Clone 159-12B, MBL Int Cat #D045-3) and anti-Rat IgG2a PE-conjugated (Biolegend, Cat #407508) were used to detect membrane-bound I-18 by flow cytometry.
In summary, mbIL18 synergizes with mbIL15 or recombinant IL15 to induce IFNγ release in T cells. IL18 constructs IL18-037 and IL18-042 show 2 to 3-fold regulation and ability to synergize with recombinant IL15 to induce IFNγ release in T cells. The IL18-042 construct shows IL18 activity also in media collected from transduced activated cells, supporting potential pleiotropic effect.
Constructs 333 and 345 were characterized in vitro.
For in vivo studies, NOD SCID gamma mice were implanted intravenously with 100,000 cells from the CD19+ Raji Burkitt's lymphoma cell line stably expressing luciferase to track tumor growth. The mice were randomized into treatment groups for equal tumor burden three (3) days post tumor implantation. Four days post tumor implantation, different cell doses of CD19-CAR-T cells bearing various IL12 constructs were treated via adoptive cell transfer (ACT). Mice were bled 7 days post ACT to provide a baseline of cytokine levels and cell expansion before dosing with ACZ with oral gavage. ACZ dosing and bleeds continued as described in
As shown in
For the scRaji study, NOD SCID gamma mice were implanted subcutaneously with 5 million Raji cells—a CD19+ Burkitt's lymphoma cell line. The mice were randomized into treatment groups for equal tumor volume (measured using digital calipers) 13 days post tumor implantation. Fourteen (14) days post tumor implantation, CD19-CAR-T cells modified with control constructs 063 (CAR-Alone), EV (Empty vector) or with construct 345 were dosed for adoptive cell transfer (ACT). Mice received continuous daily dosing of ACZ or vehicle starting on the same day as ACT. Mice were bled and measured as described in the study design (
For the PMEL study (
To summarize, IL12 was mostly localized in the tumor using membrane-bound regulated constructs, whereas regulated IL12 and IFNγ were observed systemically. In the blood, it was found that the regulated modulation hub IL12 had functional impacts. The on-state IL12 levels (in the plasma and the tumor) produced by adoptively transferred Pmel cells engineered with modulation hub IL12 constructs were closer to IL12 levels in animals receiving Pmel cells expressing constitutive mbIL12 constructs than IL12 levels in animals in which modulation hub IL12 was left in the off-state (no doses of ACZ). Likewise, phenotypes such as MHCII expression on circulating monocytes were regulated by ACZ in animals receiving Pmels cells engineered with modulation hub IL12 (
Three oligomerization concepts were tested with PDE5 as the DRD. Two control constructs IL12-229 and IL12-235 were included in the test. In IL12-274, IL12 was directly fused with CD40L and the natural shedding site of CD40L was abrogated. IL12-275 uses the DAP12 transmembrane hinge. IL12-276 was oligomerized with a collectin 7 helix trimer, except the collectin 7 was placed intracellularly. Flow cytometry analysis shown in
Tumor infiltrating lymphocytes (TILs) were isolated from tumors, expanded, and transduced with a control construct (Construct 292) containing only membrane-bound IL15 (mbIL15) and a construct containing both constitutive mbIL15 and a CA2-modulation hub regulated form of IFNα (Construct 016). Transduced cells (500,000) were transferred into a GREX device and allowed to expand for 2 weeks according to a rapid expansion protocol with or without 25 μM ACZ. At the end of that 2 weeks, the TILs were analyzed for surface abundance of IFNα using flow cytometry (BD Biosciences Cat #560097). The results are shown in
For
In another round of experiments, human TILs were expanded and engineered with lentiviral vectors to express IL15 with IFNα, IL18 (IL1 family member) (see Example 18) or TNFSF-X (TNF superfamily member). Expanded TILs were immunophenotyped and assessed for polyfunctionality by flow cytometry after CD3/CD28 stimulation. Engineered TILs were transferred into NSG mice to assess antigen-independent TIL persistence in the absence of exogenous IL2. Cytokines modified with our carbonic anhydrase 2 (CA2)-based drug responsive domain (DRD) were evaluated for control of protein levels with the CA2 ligand, acetazolamide (ACZ). Cytokine expression was evaluated in flow cytometry and Meso Scale Discovery assays.
Engineered TILs expressing both IL15 and either IFNα, IL18 or TNFSF-X showed similar fold expansion, immunophenotype, and polyfunctionality in vitro as TILs expressing only IL15. Combination cytokine-expressing TILs showed similar in vivo antigen-independent persistence in the absence of IL2 as TILs engineered with only IL15. As compared to control cells, sub-optimal cell doses of T cells expressing both IL15 and either IFNα or IL18 showed improved efficacy and TME remodeling, whereas combining IL15 with TNFSF-X resulted in significant tumor growth arrest of B16 melanoma tumors without escape.
IL15 drives expansion and persistence of cytoTIL15TM cells without IL2, and adding pleotropic and highly immune-stimulatory members of the IFN, IL1, or TNF families provides enhanced efficacy for patients with solid tumors marked by an immunosuppressive TME.
The testing protocol is shown in
HEK-293T cells were cultured in standard media (DMEM (Fisher Scientific Cat #11-960-044) with 10% FBS (Fisher Scientific Cat #10-082-147) and 1% penicillin/streptomycin (P/S, ThermoFisher Cat #15140122). HEK293T cells were transiently transfected using manufacturer's protocol with Lipofectamine 2000 and 1 μg plasmid DNA each of SOX2-001 through SOX2-006X constructs (wherein X is varied) as shown in Table 12 below. Constructs SOX2-001 and SOX2-002 are not oligomerized. Constructs SOX2-003 and SOX2-005 are trimerized with collectin 7 placed either at the N-terminus (SOX2-003) or C-terminus (SOX2-005). Similarly, SOX2-004 and SOX2-006 were tetramerized with a helix from Kv7.4. 100 μM acetazolamide was added one day after transfection, and the cells were further cultured for 1 more day. mCherry was used as a transfection marker for SOX2-001 and SOX2-002 and GFP as a transfection marker for SOX-003 through SOX2-006 and, after checking expression level by FACs, equal number of transfected cells were pelleted and lysed using T-PER Tissue protein extraction reagent (ThermoFisher cat #78510). Lysate was run on NuPAGE 4-12% Bis-Tris gel (ThermoFisher cat #NP0321BOX) and was transferred onto a nitrocellulose membrane (iBLOT2 NC regular stacks (ThermoFisher IB23001)). SOX2 was detected using anti-FOXP3 SOX2 monoclonal antibody (RnD Cat #AF2018-SP) and IRDye 800CW Goat anti-Mouse IgG (LI-COR P/N 926-32210). The results are shown in
This application claims priority to U.S. Provisional Application No. 63/262,646, filed Oct. 18, 2021 and U.S. Provisional Application No. 63/342,443, filed May 16, 2022, which are incorporated by reference herein in their entireties. The instant application contains a Sequence Listing which has been submitted electronically in XML format and is hereby incorporated by reference in its entirety. Said Sequence Listing XML, created on Oct. 18, 2022, is named 108407-1354052-October 18.xml and is 691,346 bytes in size.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US2022/046998 | 10/18/2022 | WO |
| Number | Date | Country | |
|---|---|---|---|
| 63262646 | Oct 2021 | US | |
| 63342443 | May 2022 | US |
