Infectious titration assay
By labeling immune cells with specific antibodies and using flow cytometry, the method addresses the inefficiencies of existing lentiviral vector potency assays, offering precise and efficient titer quantification for effective vector administration.
Patent Information
- Application Number
- PCT/US2025/028348
- Authority / Receiving Office
- WO · WO
- Patent Type
- Applications
- Current Assignee / Owner
- Priority Date
- 2024-05-08
- Filing Date
- 2025-05-08
- Publication Date
- 2025-11-13
AI Technical Summary
Current methods for determining lentiviral vector potency, such as PCR, are labor-intensive and insufficient for accurately quantifying infectious titers, necessitating more effective assays.
A method involving contacting immune cells infected with a viral vector with specific antibodies to label cells expressing both an immune cell surface marker and a chimeric antigen receptor, followed by flow cytometry to determine the infectious titer using a formula that calculates the percentage of positive cells.
Provides a more precise and efficient quantification of infectious titers, enabling effective administration of viral vectors based on determined potency.
Smart Images

Figure US2025028348_13112025_PF_FP_ABST
Abstract
Description
DOCKET NO: INH-032WO PATENT INFECTIOUS TITRATION ASSAY CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application claims priority to U.S. Provisional Application Ser. No. 63 / 644,297, Filed May 08, 2024, which is hereby incorporated by reference in its entirety. REFERENCE TO SEQUENCE LISTING SUBMITTED ELECTRONICALLY
[0002] 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 XML copy, created on May 07, 2025, is named “INH-032WO_SL.XML” and is 97,467 bytes in size. FIELD
[0003] Embodiments provided herein relate to the process of determining infectious titers of pharmaceutical preparations of viral vectors. BACKGROUND
[0004] Lentiviral vector (LVV) potency, as measured by transduction efficiency, is a Critical Quality Attribute (CQA) that must be monitored for every LVV sample. Current methods are labor intensive and often rely on PCR to evaluate potency, which is not always sufficient to determine specific potency. Accordingly, there is a need for assays to better quantify infectious titers. The present embodiments provides these as well as other embodiments. BRIEF SUMMARY
[0005] In some embodiments, a method of determining the infectious titer of a pharmaceutical composition comprising a viral vector is provided, wherein the viral vector comprises a nucleic acid molecule encoding for a chimeric antigen receptor comprising an antigen binding domain, the method comprising: contacting ex vivo an immune cell preparation comprising immune cells infected with the pharmaceutical composition comprising the viral vector with a first antibody and a second antibody, wherein the first antibody binds to an immune cell surface marker (ICSM) of interest on the infected immune cells and the second antibody is an idiotypic antibody that binds to the antigen binding domain of the chimeric antigen receptor to produce an antibody labeled immune cell preparation; and analyzing the IPTS / 128954004.1DOCKET NO: INH-032WO PATENT antibody labeled immune cell preparation to determine the number of cells that are positive for the immune cell surface marker of interest (ICSM+) and positive for the antigen binding domain of the chimeric antigen receptor (CAR+) to determine the infectious titer of the pharmaceutical composition comprising the virus.
[0006] In some embodiments, the infectious titer is calculated by the following formula: IU=[(%CAR+ / ICSM+) x (Total number of cells seeded in well) x (Dilution Factor)] / (Total Volume of the Inoculum and cell volume(mL)); or TU = ^% cells CAR^^ x ^# cells plated^ x total dilution mL transduction volume ^mL^
[0007] In some embodiments, the method comprises infecting a population of cells with the pharmaceutical composition comprising the virus encoding for the chimeric antigen receptor to produce the immune cell preparation infected with the pharmaceutical composition.
[0008] In some embodiments, a method of treating a disease in a subject with a pharmaceutical composition comprising a virus comprising a nucleic acid molecule encoding for a chimeric antigen receptor is provided, the method comprising: determining the infectious titer according to a method as provided for herein, and administering an effective amount of the pharmaceutical composition to the subject in an amount based on the determined infectious titer.
[0009] In some embodiments, the viral vector is a lentiviral vector pseudotyped with a VSV-G polypeptide comprising a mutation that corresponds to a mutation at position 182 of SEQ ID NO: 2.
[0010] In some embodiments, the viral vector, such as a lentiviral vector, is pseudotyped with a VSV-G polypeptide comprising a mutation that corresponds to a mutation at position 182 of SEQ ID NO: 2. BRIEF DESCRIPTION OF FIGURES
[0011] FIG.1 illustrates the general procedure for the infectious titration assay.
[0012] FIG. 2 illustrates the results of an assay variation analysis comparing plating cells by hand versus use of an automated CyBio Felix plating system.
[0013] FIG. 3A, 3B, 3C, and 3D illustrate the results of an assay variation analysis comparing hand pipetting for media refresh versus use of an automated CyBio Felix system. FIG. 3A illustrates the results of the Felix system using a high aspiration height. FIG. 3B illustrates the results of the Felix system using a low aspiration height. FIG.3C illustrates the -2- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT results of manual pipetting for media refresh. FIG. 3D illustrates the comparison of readout across all parameters.
[0014] FIG. 4 illustrates the results comparing the automated assay versus traditional manual assay. DETAILED DESCRIPTION
[0015] Unless otherwise defined, scientific and technical terms used herein have the meanings that are commonly understood by those of ordinary skill in the art. In the event of any latent ambiguity, definitions provided herein take precedent over any dictionary or extrinsic definition. Unless otherwise required by context, singular terms shall include pluralities and plural terms shall include the singular. The use of “or” means “and / or” unless stated otherwise. The use of the term “including,” as well as other forms, such as “includes” and “included,” is not limiting.
[0016] Generally, nomenclature used in connection with cell and tissue culture, molecular biology, immunology, microbiology, genetics and protein and nucleic acid chemistry and hybridization described herein is well-known and commonly used in the art. The methods and techniques provided herein are generally performed according to conventional methods well known in the art and as described in various general and more specific references that are cited and discussed throughout the present specification unless otherwise indicated. Enzymatic reactions are performed according to manufacturer’s specifications, as commonly accomplished in the art or as described herein. The nomenclatures used in connection with, and the laboratory procedures and techniques of, analytical chemistry, synthetic organic chemistry, and medicinal and pharmaceutical chemistry described herein are those well-known and commonly used in the art.
[0017] That the disclosure may be more readily understood, select terms are defined below.
[0018] As used herein, the terms “a” or “an” means that “at least one” or “one or more” unless the context clearly indicates otherwise.
[0019] As used herein, the term “about” means that the numerical value is approximate and small variations would not significantly affect the practice of the disclosed embodiments. Where a numerical limitation is used, unless indicated otherwise by the context, “about” means the numerical value can vary by ±10% and remain within the scope of the disclosed embodiments. Additionally, where a phrase recites “about x to y,” the term “about” modifies -3- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT both x and y and can be used interchangeably with the phrase “about x to about y” unless context dictates differently.
[0020] As used herein, the term “individual” or “subject,” or “patient” used interchangeably, means any animal, including mammals, such as mice, rats, other rodents, rabbits, dogs, cats, swine, cattle, sheep, horses, or primates, such as humans.
[0021] As used herein, the terms “comprising” (and any form of comprising, such as “comprise”, “comprises”, and “comprised”), “having” (and any form of having, such as “have” and “has”), “including” (and any form of including, such as “includes” and “include”), or “containing” (and any form of containing, such as “contains” and “contain”), are inclusive or open-ended and do not exclude additional, unrecited elements or method steps. Any step or composition that uses the transitional phrase of “comprise” or “comprising” can also be said to describe the same with the transitional phase of “consisting of” or “consists.”
[0022] As used herein, the phrase “purified viral vector” is defined as viral vector which has been purified from cell culture harvest and is using at least one chromatography step.
[0023] As used herein, the term “sterile filtered” as used in reference to a pharmaceutical composition comprising a viral vector refers to a pharmaceutical composition that has been sterilized by filtration to remove infectious agents other than the one of interest that is intended to be in the pharmaceutical composition.
[0024] As used herein, the term “contacting” means bringing together of two elements in an in vitro system or an in vivo system. For example, “contacting” virus or vector described herein with an individual or patient or cell includes the administration of the virus to an individual or patient, such as a human, as well as, for example, introducing a virus into a sample containing a cell or population of cells.
[0025] As used herein, the term “fused” or “linked” when used in reference to a protein having different domains or heterologous sequences means that the protein domains are part of the same peptide chain that are connected to one another with either peptide bonds or other covalent bonding. The domains or section can be linked or fused directly to one another or another domain or peptide sequence can be between the two domains or sequences and such sequences would still be considered to be fused or linked to one another. In some embodiments, the various domains or proteins provided for herein are linked or fused directly to one another or a linker sequences, such as the glycine / serine sequences described herein link the two domains together.
[0026] A “disease” in an animal is a state of health wherein the animal cannot maintain homeostasis, and wherein if the disease is not ameliorated then the animal’s health continues -4- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT to deteriorate. In contrast, a “disorder” in an animal is a state of health in which the animal is able to maintain homeostasis, but in which the animal’s state of health is less favorable than it would be in the absence of the disorder. Left untreated, a disorder does not necessarily cause a further decrease in the animal’s state of health.
[0027] “Effective amount” or “therapeutically effective amount” are used interchangeably herein, and refer to an amount of a compound, formulation, material, or composition, as described herein effective to achieve a particular biological result or provides a therapeutic or prophylactic benefit. Such results may include, but are not limited to an amount that when administered to a mammal, causes a detectable level of immune cell activation compared to the immune cell activation detected in the absence of the composition. The immune response can be readily assessed by a plethora of art-recognized methods. The skilled artisan would understand that the amount of the composition administered herein varies and can be readily determined based on a number of factors such as the disease or condition being treated, the age and health and physical condition of the mammal being treated, the severity of the disease, the particular compound being administered, and the like.
[0028] “Encoding” refers to the inherent property of specific sequences of nucleotides in a polynucleotide, such as a gene, a cDNA, or an mRNA, to serve as templates for synthesis of other polymers and macromolecules in biological processes having either a defined sequence of nucleotides (i.e., rRNA, tRNA and mRNA) or a defined sequence of amino acids and the biological properties resulting therefrom. Thus, a gene encodes a protein if transcription and translation of mRNA corresponding to that gene produces the protein in a cell or other biological system. Both the coding strand, the nucleotide sequence of which is identical to the mRNA sequence and is usually provided in sequence listings, and the non-coding strand, used as the template for transcription of a gene or cDNA, can be referred to as encoding the protein or other product of that gene or cDNA.
[0029] “Expression vector” refers to a vector comprising a recombinant polynucleotide comprising expression control sequences operatively linked to a nucleotide sequence to be expressed. An expression vector comprises sufficient cis-acting elements for expression; other elements for expression can be supplied by the host cell or in an in vitro expression system. Expression vectors include all those known in the art, such as cosmids, plasmids (e.g., naked or contained in liposomes) and viruses (e.g., Sendai viruses, lentiviruses, retroviruses, adenoviruses, and adeno-associated viruses) that incorporate the recombinant polynucleotide.
[0030] As used herein, the phrase “ex vivo” in reference to a cell being transduced, transfected or transformed ex vivo, refers to a cell being transduced, transfected or transformed -5- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT outside of the subject, that is with the cells being removed from the subject before such cells are transduced, transfected or transformed.
[0031] As used herein, “filter” refers to any substance through which a solution or composition is passed to remove portions (e.g.) of the solution or composition. Therefore, “filter” is not meant to be limited to a membrane filter, but also includes any substance of any thickness through with the solution or composition is passed. Accordingly, the term “filter” may include, but not be limited to, membranes, such as PES, nylon, or PVDF membranes; membrane chromatography units such as Sartobind Q, Mustang Q, and the like; or stationary phases such as an ion exchange stationary phase (e.g. cross linked polymer resin such as divinylbenzene cross-linked polystyrene), affinity stationary phase (e.g. nickel resin, streptavidin resin, glutathione conjugated resin, protein A or protein G conjugated resin, and the like), hydrophobic stationary phase (e.g. silica resin bonded with butyl, phenyl, ether, amide, or propyl ligands), size exclusion stationary phase (e.g. silica resin with appropriate diameter and pore size), or any combination thereof (i.e. multimodal chromatography). In some embodiments, the “filter” is a resin, such as a chromatography resin as provided for herein. Similarly, the term “chromatographic filter” refers to any substance that may be used for chromatographic separation of a solution or composition. Therefore, “chromatographic filter” is not meant to be limited to a membrane filter, but also includes any substance of any thickness through with the solution or composition is passed. Accordingly, the term “chromatographic filter” may include, but not be limited to, membranes, such as PES, nylon, or PVDF membranes; membrane chromatography units such as Sartobind Q, Mustang Q, and the like; or stationary phases such as an ion exchange stationary phase (e.g. cross linked polymer resin such as divinylbenzene cross-linked polystyrene), affinity stationary phase (e.g. nickel resin, streptavidin resin, glutathione conjugated resin, protein A or protein G conjugated resin, and the like), hydrophobic stationary phase (e.g. silica resin bonded with butyl, phenyl, ether, amide, or propyl ligands), size exclusion stationary phase (e.g. silica resin with appropriate diameter and pore size), or any combination thereof (i.e. multimodal chromatography).
[0032] “Identity” as used herein refers to the subunit sequence identity between two polymeric molecules such as between two nucleic acid or amino acid molecules, such as, between two polynucleotide or polypeptide molecules. When two amino acid sequences have the same residues at the same positions; e.g., if a position in each of two polypeptide molecules is occupied by an Arginine, then they are identical at that position. The identity or extent to which two amino acid or two nucleic acid sequences have the same residues at the same -6- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT positions in an alignment is often expressed as a percentage. The identity between two amino acid or two nucleic acid sequences is a direct function of the number of matching or identical positions; e.g., if half of the positions in two sequences are identical, the two sequences are 50% identical; if 90% of the positions (e.g., 9 of 10), are matched or identical, the two amino acids sequences are 90% identical.
[0033] By "substantially identical" is meant a polypeptide or nucleic acid molecule exhibiting at least 50% identity to a reference amino acid sequence (for example, any one of the amino acid sequences described herein) or nucleic acid sequence (for example, any one of the nucleic acid sequences described herein). In some embodiments, such a sequence is at least 60%, 80% or 85%, or 90%, 95% or even 99% identical at the amino acid level or nucleic acid to the sequence used for comparison. Other percentages of identity in reference to specific sequences are described herein.
[0034] Sequence identity can be measured / determined using sequence analysis software (for example, Sequence Analysis Software Package of the Genetics Computer Group, University of Wisconsin Biotechnology Center, 1710 University Avenue, Madison, Wis. 53705, BLAST, BESTFIT, GAP, or PILEUP / PRETTYBOX programs). Such software matches identical or similar sequences by assigning degrees of homology to various substitutions, deletions, and / or other modifications. Conservative substitutions typically include substitutions within the following groups: glycine, alanine; valine, isoleucine, leucine; aspartic acid, glutamic acid, asparagine, glutamine; serine, threonine; lysine, arginine; and phenylalanine, tyrosine. In an exemplary approach to determining the degree of identity, a BLAST program may be used, with a probability score between e3 and e100 indicating a closely related sequence. In some embodiments, sequence identity is determined by using BLAST with the default settings.
[0035] To the extent embodiments provided for herein, include compositions comprising various proteins, these proteins may, in some instances, comprise amino acid sequences that have sequence identity to the amino acid sequences disclosed herein. Therefore, in certain embodiments, depending on the particular sequence, the degree of sequence identity is preferably greater than 50% (e.g.60%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more) to the SEQ ID NOs disclosed herein. In addition to these percentages, other percentages of identity are provided for herein. Identity between polypeptides can be determined by the Smith-Waterman homology search algorithm as implemented in the MPSRCH program (Oxford Molecular), using an affine gap search with parameters gap open penalty – 12 and gap extension penalty = 1. These proteins may, compared -7- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT to the disclosed proteins, include one or more (e.g.1, 2, 3, 4, 5, 6, 7, 8, 9, 10, etc.) conservative amino acid replacements i.e. replacements of one amino acid with another which has a related side chain. Genetically-encoded amino acids are generally divided into four families: (1) acidic i.e. aspartate, glutamate; (2) basic i.e. lysine, arginine, histidine; (3) non polar i.e. alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan; and (4) uncharged polar i.e. glycine, asparagine, glutamine, cysteine, serine, threonine, tyrosine. Phenylalanine, tryptophan, and tyrosine are sometimes classified jointly as aromatic amino acids. In general, Substitution of single amino acids within these families does not have a major effect on the biological activity. The proteins may have one or more (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, etc.) single amino acid deletions relative to the disclosed protein sequences. The proteins may also include one or more (e.g.1, 2, 3, 4, 5, 6, 7, 8, 9, 10, etc.) insertions (e.g. each of 1, 2, 3, 4 or 5 amino acids) relative to the disclosed protein sequences.
[0036] As used herein, the phrase “in vivo” in reference to a cell being transduced, transfected or transformed in vivo, refers to a cell being transduced, transfected or transformed in the subject without the cells being removed from the subject before such cells are transduced, transfected or transformed.
[0037] “Isolated” means altered or removed from the natural state. For example, a nucleic acid or a peptide naturally present in a living animal is not “isolated,” but the same nucleic acid or peptide partially or completely separated from the coexisting materials of its natural state is “isolated.” An isolated nucleic acid or protein can exist in substantially purified form, or can exist in a non-native environment such as, for example, a host cell.
[0038] A “lentivirus” as used herein refers to a genus of the Retroviridae family that is able to infect non-dividing cells. Non-limiting examples of lentiviruses are HIV, SIV, and FIV. Vectors or viral-like particles derived from lentiviruses can be used to transduce cells and deliver genes or other molecules and have them expressed in a cell either in vitro, ex-vivo, or in vivo.
[0039] By the term “modified” as used herein, is meant a changed state or structure of a molecule or cell as provided herein. Molecules may be modified in many ways, including chemically, structurally, and functionally, such as mutations, substitutions, insertions, or deletions (e.g. internal deletions truncations). Cells may be modified through the introduction of nucleic acids or the expression of heterologous proteins.
[0040] By the term “modulating,” as used herein, is meant mediating an increase or decrease in the level of a response in a subject compared with the level of a response in the subject in the absence of a treatment or compound, and / or compared with the level of a response -8- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT in an otherwise identical but untreated subject. The term encompasses perturbing and / or affecting a native signal or response thereby mediating a beneficial therapeutic response in a subject, such as, a human.
[0041] Unless otherwise specified, a “nucleotide sequence encoding an amino acid sequence” includes all nucleotide sequences that are degenerate versions of each other and that encode the same amino acid sequence. The phrase nucleotide sequence that encodes a protein or an RNA may also include introns to the extent that the nucleotide sequence encoding the protein may in some version contain an intron(s).
[0042] The term “oligonucleotide” typically refers to short polynucleotides. It will be understood that when a nucleotide sequence is represented by a DNA sequence (i.e., A, T, C, G), this also provides the corresponding RNA sequence (i.e., A, U, C, G) in which “U” replaces “T.”
[0043] “Parenteral” administration of a composition includes, e.g., subcutaneous (s.c.), intravenous (i.v.), intramuscular (i.m.), or intrasternal injection, intrathecal, or infusion techniques.
[0044] The term “polynucleotide” as used herein is defined as a chain of nucleotides. Furthermore, nucleic acids are polymers of nucleotides. Thus, the terms “nucleic acids” and “polynucleotides” as used herein are interchangeable. As used herein polynucleotides include, but are not limited to, all nucleic acid sequences which are obtained by any methods available in the art, including, without limitation, recombinant methods, i.e., the cloning of nucleic acid sequences from a recombinant library or a cell genome, using cloning technology and PCR, and the like, and by synthetic means.
[0045] As used herein, the terms “peptide,” “polypeptide,” and “protein” are used interchangeably, and refer to a compound comprised of a plurality of amino acid residues covalently linked by peptide bonds. As used herein, the term refers to both short chains, which also commonly are referred to in the art as peptides, oligopeptides and oligomers, for example, and to longer chains, which generally are referred to in the art as proteins, of which there are many types. “Polypeptides” include, for example, biologically active fragments, substantially homologous polypeptides, oligopeptides, homodimers, heterodimers, variants of polypeptides, modified polypeptides, derivatives, analogs, fusion proteins, among others. The polypeptides include natural peptides, recombinant peptides, synthetic peptides, or a combination thereof.
[0046] The term “pseudotyped” or “pseudotyped viral particle”, as used herein, refers to a viral particle bearing glycoproteins derived from other viruses having envelopes or a viral vector encoding envelope glycoproteins from a virus that is different from the parental virus. -9- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT The host range of the vector particles can thus be expanded or altered depending on the type of cell surface receptor used by the glycoprotein. For example, a virus can be pseudotyped with a VSV-G mutant protein as provided for herein.
[0047] By the term “specifically binds,” as used herein with respect to an antibody, is meant an antibody which recognizes a specific antigen, but does not substantially recognize or bind other molecules in a sample. For example, an antibody that specifically binds to an antigen from one species may also bind to that antigen from one or more species. But, such cross- species reactivity does not itself alter the classification of an antibody as specific. In another example, an antibody that specifically binds to an antigen may also bind to different allelic forms of the antigen. However, such cross reactivity does not itself alter the classification of an antibody as specific. In some instances, the terms “specific binding” or “specifically binding,” can be used in reference to the interaction of an antibody, a protein, or a peptide with a second chemical species, to mean that the interaction is dependent upon the presence of a particular structure (e.g., an antigenic determinant or epitope) on the chemical species; for example, an antibody recognizes and binds to a specific protein structure rather than to proteins generally. If an antibody is specific for epitope “A”, the presence of a molecule containing epitope A (or free, unlabeled A), in a reaction containing labeled “A” and the antibody, will reduce the amount of labeled A bound to the antibody. In some embodiments, the targeting moieties described herein that can be used to target the viral particles comprising the mutant VSV-G protein, or other viral structural proteins used to pseudotype a virus, can specifically bind to their target.
[0048] The term “therapeutic” as used herein means a treatment and / or prophylaxis. A therapeutic effect is obtained by suppression, remission, or eradication of a disease state.
[0049] The term “transfected” or “transformed” or “transduced” as used herein refers to a process by which exogenous nucleic acid is transferred or introduced into a cell. A “transfected” or “transformed” or “transduced” cell is one which has been transfected, transformed or transduced with exogenous nucleic acid. The cell includes the primary subject cell and its progeny. In some embodiments, the transfection, transformation, or transduction is performed or occurs in vivo.
[0050] A “vector” is a composition of matter which comprises an isolated nucleic acid encoding a protein or a peptide. Numerous vectors are known in the art including, but not limited to, linear polynucleotides, plasmids, DNA, and RNA. Examples of viral vectors include, but are not limited to, Sendai viral vectors, adenoviral vectors, adeno-associated virus vectors, retroviral vectors, lentiviral vectors, and the like. -10- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT
[0051] As used herein, unless otherwise specified, the terms “virus”, “viral vector”, and “viral particle” are used interchangeably. Similarly, unless otherwise specified, the terms “lentivirus”, “lentiviral vector” and “lentiviral particle” are used interchangeably.
[0052] A “carrier” or “delivery vehicle” includes viral particles, viruses, polylysine compounds, and liposomes, which facilitate transfer of nucleic acid into cells. A carrier or delivery vehicle can also be used to deliver a protein or peptide to a cell.
[0053] Ranges: throughout this disclosure, various aspects of the embodiments can be presented in a range format. It should be understood that the description in range format is merely for convenience and brevity and should not be construed as an inflexible limitation. Accordingly, the description of a range should be considered to have specifically disclosed all the possible subranges as well as individual numerical values within that range. For example, description of a range such as from 1 to 6 should be considered to have specifically disclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numbers within that range, for example, 1, 2, 2.7, 3, 4, 5, 5.3, and 6. This applies regardless of the breadth of the range. Unless otherwise explicitly stated to the contrary, a range that is disclosed also includes the endpoints of the range.
[0054] Without being bound to any particular theory, standard viral purification techniques tend to result in a loss of viral product during filtration. This is especially the case when the viral product is concentrated prior to sterile filtration, as is standard practice. Passing a pre-flush protein solution through the sterile filter prior to filtration of the viral product results in increased viral yields, possibly due to the protein solution preventing the viral product from becoming trapped in the filter due to charge interactions. Further, performing sterile filtration prior to concentrating the viral product was also found to increase product yields. Assays
[0055] In some embodiments, methods of determining the infectious titer of a composition, such as a pharmaceutical composition, comprising a virus are provided. In some embodiments, the virus, which can be referred to as a viral vector, comprises a nucleic acid molecule encoding for a chimeric antigen receptor. Chimeric antigen receptors are known in the art and for the purposes of this application comprise an extracellular domain that binds to a target antigen. This can be referred to as an antigen binding domain.
[0056] In some embodiments, the composition or pharmaceutical is sterile filtered. The sterile filtration should not significantly reduce the infectivity of the virus that is intended to be in the pharmaceutical composition that is to be administered to a subject. In some embodiments, the pharmaceutical composition is sterile filtered according to the embodiments -11- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT and methods provided for in PCT Application No. PCT / US2024 / 014002, filed February 1, 2024, which is hereby incorporated by reference in its entirety.
[0057] In some embodiments, the method comprises contacting ex vivo or in vitro an immune cell preparation comprising immune cells infected with the pharmaceutical composition with a first antibody and a second antibody, wherein the first antibody binds to an immune cell surface marker (ICSM) of interest and the second antibody is an idiotypic antibody that binds to the antigen binding domain of the chimeric antigen receptor to produce an antibody labeled immune cell preparation.
[0058] In some embodiments, the immune cell surface marker of interest is CD7, CD8, cKit (CD117), CD4, CD3, CD5, CD6, CD2, TCR alpha, TCR beta, TCR gamma, TCR delta, CD10, CD34, CD110, CD33, CD14, CD68, CCR7, CD62L, CD25, CCR2, CCR3, CCR4, CCR5, CCR6, CCR7, or CXCR3, A glycosylated CD43 epitope expressed on acute leukemia or lymphoma but not on hematopoietic progenitors; A glycosylated CD43 epitope expressed on non-hematopoietic cancers; A kinase anchor protein 4 (AKAP-4); Adrenoceptor beta 3 (ADRB3); AFP; Anaplastic lymphoma kinase (ALK); Androgen receptor; Angiopoietin- binding cell surface receptor 2 (Tie 2); Auto antibody to desmoglein 1 (Dsgl); Auto antibody to desmoglein 3 (Dsg3); B7H3 (CD276); Biotin; Bone marrow stromal cell antigen 2 (BST2); BST1 / CD157; Cancer / testis antigen 1 (NY-ESO-1); Cancer / testis antigen 2 (LAGE-la); Carbonic anhydrase IX (CA1X); Carcinoembryonic antigen (CEA); CCCTC-Binding Factor (Zinc Finger Protein)-Like (BORIS or Brother of the Regulator of lmprinted Sites); CCR4; CD5; CD19; CD20; CD22; CD24; CD30; CD32 (FCGR2A); CD33; CD34; CD38; CD44v6; CD72; CD79a; CD79b; CD97; CD99; CD123; CD171; CD179a; CD179b-IGLll; CD200R; CD276 / B7H3; CD300 molecule-like family member f (CD300LF); CDH1-CD324; CDH6; CDH17; CDH19; Chromosome X open reading frame 61 (CXORF61); Claudin 6 (CLDN6); Claudinl8.2 (CLD18A2 or CLDN18A.2); CMV pp65; C-MYC epitope Tag; Cripto; CS1 (also referred to as CD2 subset 1 or CRACC or SLAMF7 or CD319 or 19A24); CSF2RA (GM- CSFR-alpha); C-type lectin domain family 12 member A (CLEC12A); C-type lectin-like molecule-1 (CLL-1 or CLECL1); Cyclin Bl; Cytochrome P450 IB 1 (CYP1B 1); DLL3; EBV- EBNA3c; EGF-bke module- containing mucin-like hormone receptor-like 2 (EMR2); Elongation factor 2 mutated (ELF2M); Ephrin B2; Ephrin type-A receptor 2 (EphA2); Epidermal growth factor receptor (EGFR); Epidermal growth factor receptor variant III (EGFRviii); Epithelial cell adhesion molecule (EPCAM); ERG; ETS translocation-variant gene 6 located on chromosome 12p (ETV6-AML); Fc fragment of IgA receptor (FCAR or CD89); Fc receptor-like 5 (FCRL5); Fibroblast activation protein alpha (FAP); FITC; Fms Like -12- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT Tyrosine Kinase 3 (FLT3); Folate receptor alpha (FRa or FR1); Folate receptor beta (FRb); Follicle stimulating hormone receptor (FSHR); Fos-related antigen 1; Fucosyl-GMl; G protein coupled receptor class C group 5 member D (GPRC5D); G protein-coupled receptor 20 (GPR20); GAD; Ganglioside G2 (GD2) ; Ganglioside GD3 (aNeu5Ac(2-8)aNeu5Ac(2- 3)bDGalp(l-4 )bDGlcp(l-l)Cer); Ganglioside GM3 (aNeu5Ac(2-3)bDClalp(l- 4)bDGlcp(l- l)Cer); GD3; GFRalpha4; Glycoprotein 100 (gplOO); Glypican-3 (GPC3); Gonadotropin Hormone receptor (CGHR or GR); GpA33; GpNMB; GPRC5D; Guanylyl cyclase C (GCC); Heat shock protein 70-2 mutated (mut hsp70-2); Hepatitis A virus cellular receptor 1 (HAVCR1); Hexasaccharide portion of globoH glycoceramide (GloboH); High molecular weight-melanoma associated antigen (HMWMAA); HIV1 envelope glycoprotein; HLA; HLA- DOA; HLA-A; HLA-A2; HLA-B; HLA-C; HLA-DM; HLA-DOB; HLA-DP; HLA-DQ; HLA- DR; HLA-G; HTLVl-Tax; Human papilloma virus E6 (HPV E6); Human papilloma virus E7 (HPV E7); Human Telomerase reverse transcriptase (hTERT); IgE; IL13Ra2; ILl lRa; Immunoglobulin lambda-like polypeptide 1 (IGLL1); Influenza A hemagglutinin (HA); Insulin-like growth factor 1 receptor (IGF-I receptor); Interleukin 11 receptor alpha (IL-llRa); Interleukin- 13 receptor subunit alpha-2 (IL-13Ra2 or CD213A2); Intestinal carboxyl esterase; KIT (CD117); KSHV K8.1; KSHV-gH; LAMP1 ; Legumain; Leukocyte immunoglobulin-like receptor subfamily A member 2 (LILRA2); Leukocyte-associated immunoglobulin-like receptor 1 (LAIR1); Leutenizing hormone receptor (LHR); Lewis(Y) antigen; Lews Ag; Livl; Locus K 9 (LY6K); Low conductance chloride channel; Lymphocyte antigen 6 complex; Lymphocyte antigen 75 (LY75); Lymphocyte-specific protein tyrosine kinase (LCK); Mammary gland differentiation antigen (NY-BR-1); Melanoma antigen recognized by T cells 1 (MelanA or MARTI); Melanoma- associated antigen 1 (MAGE-A1); Melanoma cancer testis antigen-1 (MAD-CT-1); Melanoma cancer testis antigen-2 (MAD-CT-2); Melanoma inhibitor of apoptosis (ML-IAP); Mesothelin; MPL; Mucin 1 cell surface associated (MUC1); N-Acetyl glucosaminyl-transferase V (NA17); Nectin-4; Neural cell adhesion molecule (NCAM); NKG2D; NYBR1; O-acetyl-GD2 ganglioside (OAcGD2); Olfactory receptor 51E2 (OR51E2); Oncogene fusion protein consisting of breakpoint cluster region (BCR) and Abelson murine leukemia viral oncogene homolog 1 (Abl) (bcr-abl); P53 mutant; Paired box protein Pax-3 (PAX3); Paired box protein Pax-5 (PAX5); Pannexin 3 (PANX3); PDL1; P-glycoprotein; Placenta-specific 1 (PLAC1); Platelet-derived growth factor receptor beta (PDGFR-beta); Polysialic acid; Proacrosin binding protein sp32 (OY-TES1); Prostase; Prostate carcinoma tumor antigen-1 (PCT A-l or Galectin 8); Prostate stem cell antigen (PSCA); Prostate-specific membrane antigen (PSMA); Prostatic acid phosphatase (PAP); Prostein; Protease Serine 21 -13- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT (Testisin or PRSS21); Proteasome (Prosome Macropain) Subunit Beta Type 9 (LMP2); PTK7; Ras G12V; Ras Homolog Family Member C (RhoC); Rat sarcoma (Ras) mutant; Receptor for Advanced Gly cation Endproducts (RAGE-1); Receptor tyrosine kinase-like orphan receptor 1 (ROR1); Receptor tyrosine-protein kinase ERBB2 or Her-22 / neu; Renal ubiquitous 1 (RU1); Renal ubiquitous 2 (RU2); Sarcoma translocation breakpoints; Serine 2 (TMPRSS2) ETS fusion gene; Sialyl Lewis adhesion molecule (sLe); SLAMF4; SLAMF6; Slea (CA19.9 or Sialyl Lewis Antigen); Sperm protein 17 (SPA17); Squamous Cell Carcinoma Antigen Recognized By T Cells 3 (SART3); Stage-specific embryonic antigen-4 (SSEA-4); STEAP1; Survivin; Synovial sarcoma X breakpoint 2 (SSX2); TCR Gamma Alternate Reading Frame Protein (TARP); TCR-beta1 chain; TCR-beta2 chain; TCR-delta chain; TCR-gamma chain; TCRgamma-delta; Telomerase; TGFbetaR2; The antigen recognized by TNT antibody; Thyroid stimulating hormone receptor (TSHR); Timl- / HVCR1; Tissue Factor 1 (TF1); Tn ag; Tn antigen ((Tn Ag) or (GalNAca-Ser / Thr)); TNF receptor family member B cell maturation (BCMA); Transglutaminase 5 (TGS5); Transmembrane protease; TROP2; Tumor endothelial marker 1 (TEM1 / CD248); Tumor endothelial marker 7-related (TEM7R); Tumor protein p53 (p53); Tumor-associated glycoprotein 72 (TAG72); Tyrosinase; Tyrosinase-related protein 2 (TRP-2); Uroplakin 2 (UPK2); Vascular endothelial growth factor receptor 2 (VEGFR2); V- myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog (MYCN); Wilms tumor protein (WT1); or X Antigen Family Member 1A (XAGE1). In some embodiments, the immune cell surface marker of interest is CD7. In some embodiments, the immune cell surface marker of interest is CD8.
[0059] In some embodiments, the immune cell preparation comprises T cells. In some embodiments, the T cells are SupT1 cells (Stanford University Pediatric T-cell line 1). The immune cell preparation can be prepared after the immune cells are cultured with virus or viral vector present in the pharmaceutical composition.
[0060] In some embodiments, the methods further comprise analyzing the antibody labeled immune cell preparation to determine the number of cells that are positive for the immune cell surface marker of interest (ICSM+) and positive for the antigen binding domain of the chimeric antigen receptor (CAR+) to determine the infectious titer of the pharmaceutical composition comprising the virus.
[0061] In some embodiments, the infectious titer is transduction units (“TU”), which can be referred to as infectious units / mL (“IU”). In some embodiments, wherein the infectious titer is calculated by the following formula: -14- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT IU=[(%CAR+ / ICSM+) x (Total number of cells seeded in well) x (Dilution Factor)] / (Total volume of inoculum added to cells and cell volume (mL)); or can be represented by the formula of ^^^^ ^
[0062] In some embodiments, the first antibody is labeled with a first label and the second antibody is labeled with a second label, wherein the first label and the second label are different. The labels can be any labels, such as a fluorescent labels that emit at different wavelengths. The label can also be a light emitting label.
[0063] The analysis of the preparation to determine the infectious titer can be performed by flow cytometry to detect the cells that are ICSM+ and CAR+.
[0064] In some embodiments, the cells are fixed prior to being analyzed with flow cytometry. In some embodiments, the fixing the cells comprises heat killing the cells. In some embodiments, the heat killing the cells comprises heating the cells at a temperature of about 75 to about 85 C, or about 78 to about 82 C. In some embodiments, the cells are heated at a temperature of about 80 C (+ / - 2 C). In some embodiments, the cells are heated for about 3 to about 5 minutes. In some embodiments, the cells are fixed in formaldehyde. In some embodiments, the cells are fixed in formaldehyde and PBS. In some embodiments, the cells are fixed in 3.7% formaldehyde and PBS (e.g. 10% Formalin). In some embodiments, the control is heat killed, but not the cells to be analyzed that are found to be ICSM+ and CAR+.
[0065] In some embodiments, the methods comprise producing the immune cell preparation. In some embodiments, the methods comprise infecting a population of cells, such as immune cells (e.g. T cells) with the pharmaceutical composition comprising the virus or viral vector encoding for the chimeric antigen receptor to produce the immune cell preparation infected with the pharmaceutical composition. In some embodiments, the virus is a lentivirus, such as but not limited to a pseudotyped lentivirus. Non-limiting examples of such viruses are provided for herein. In some embodiments, the immune cells or T cells are CD7+ cells.
[0066] As provided for herein, the first antibody can be used to gate the cells to ensure that the target cell population is being analyzed appropriately. Thus, in some embodiments, the first antibody specifically binds to CD7 or CD8. The first antibody, however, can bind to any immune cell surface marker of interest. Non-limiting examples are provided for herein. -15- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT
[0067] The second antibody can be utilized to bind to the antigen binding domain of the chimeric antigen receptor. The antigen binding domain can be in the form, for example, of a scFv. The second antibody can be idiotypic, which means that is specific for the antigen binding domain of the chimeric antigen receptor and will not bind to any antibody. Accordingly, in some embodiments, the antigen binding domain of the CAR binds to CD19 or CD20.
[0068] The preparations that are analyzed according to the embodiments provided for herein can be used to treat patients for various cancers. Thus, in some embodiments, methods of treating a disease, such as cancer, in a subject with a pharmaceutical composition are provided. In some embodiments, the pharmaceutical composition comprises a virus comprising a nucleic acid molecule encoding for a chimeric antigen receptor. In some embodiments, the method comprises determining the infectious titer according to the embodiments provided for herein; and administering an effective amount of the pharmaceutical composition to the subject in an amount based on the determined infectious titer. In some embodiments, pharmaceutical composition is administered parenterally. VIRAL VECTORS
[0069] In some embodiments, the pharmaceutical composition comprises a virus, such as a pseudotyped virus. In some embodiments, pseudotyped viral vector comprises a VSV-G polypeptide.
[0070] In some embodiments, a VSV-G protein is provided that comprises a mutation at position 198 as compared to SEQ ID NO: 1 or at position 182 as compared to SEQ ID NO: 2. SEQ ID NO: 1 is the full length protein and SEQ ID NO: 2 is the ectodomain of the VSV- G protein. The 16-mer signal peptide of MKCLLYLAFLFIGVNC (SEQ ID NO: 65) as shown at the N-terminus of SEQ ID NO: 1 is cleaved leaving a protein of SEQ ID NO: 2. Thus, although a mutation may be referred to in the context of SEQ ID NO: 2, it should be understood to also be made in the context of SEQ ID NO: 1, which contains the leader sequence, and thus would be a position number that is 16 more than the position recited for SEQ ID NO: 2. In some embodiments, the mutation inhibits or decreases the binding of the VSV-G protein to the LDL receptor (LDL-R). In some embodiments, the mutation is a I182D mutation as compared to SEQ ID NO: 2. In some embodiments, the mutation is a I182E mutation as compared to SEQ ID NO: 2.
[0071] In some embodiments, a VSV-G protein is provided that comprises a mutation at position 198 as compared to SEQ ID NO: 10 or at position 182 as compared to SEQ ID NO: 11. SEQ ID NO: 10 is the full length protein and SEQ ID NO: 11 is the ectodomain of the -16- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT VSV-G protein. The 16-mer signal peptide of MLSYLIFALVVSPILG (SEQ ID NO: 66) as shown at the N-terminus of SEQ ID NO: 10 is cleaved leaving a protein of SEQ ID NO: 11. Thus, although a mutation may be referred to in the context of SEQ ID NO: 11, it should be understood to also be made in the context of SEQ ID NO: 10, which contains the leader sequence, and thus would be a position number that is 16 more than the position recited for SEQ ID NO: 11. In some embodiments, the mutation inhibits or decreases the binding of the VSV-G protein to the LDL receptor (LDL-R). In some embodiments, the mutation is a T182D mutation as compared to SEQ ID NO: 11. In some embodiments, the mutation is a T182E mutation as compared to SEQ ID NO: 11.
[0072] In some embodiments, a VSV-G protein is provided that comprises a mutation at position 198 as compared to SEQ ID NO: 12 or at position 182 as compared to SEQ ID NO: 13. SEQ ID NO: 12 is the full length protein and SEQ ID NO: 13 is the ectodomain of the VSV-G protein. The 16-mer signal peptide of MLRLFLFCFLALGAHS (SEQ ID NO: 67) as shown at the N-terminus of SEQ ID NO: 12 is cleaved leaving a protein of SEQ ID NO: 13. Thus, although a mutation may be referred to in the context of SEQ ID NO: 13, it should be understood to also be made in the context of SEQ ID NO: 12, which contains the leader sequence, and thus would be a position number that is 16 more than the position recited for SEQ ID NO: 13. In some embodiments, the mutation inhibits or decreases the binding of the VSV-G protein to the LDL receptor (LDL-R). In some embodiments, the mutation is a A182D mutation as compared to SEQ ID NO: 13. In some embodiments, the mutation is a A182E mutation as compared to SEQ ID NO: 13.
[0073] In some embodiments, a VSV-G protein is provided that comprises a mutation at position 203 as compared to SEQ ID NO: 14 or at position 182 as compared to SEQ ID NO: 15. SEQ ID NO: 14 is the full length protein and SEQ ID NO: 15 is the ectodomain of the VSV-G protein. The 21-mer signal peptide of MKMKMVIAGLILCIGILPAIG (SEQ ID NO: 68) as shown at the N-terminus of SEQ ID NO: 14 is cleaved leaving a protein of SEQ ID NO: 15. Thus, although a mutation may be referred to in the context of SEQ ID NO: 15, it should be understood to also be made in the context of SEQ ID NO: 14, which contains the leader sequence, and thus would be a position number that is 21 more than the position recited for SEQ ID NO: 15. In some embodiments, the mutation inhibits or decreases the binding of the VSV-G protein to the LDL receptor (LDL-R). In some embodiments, the mutation is a V182D mutation as compared to SEQ ID NO: 15. In some embodiments, the mutation is a V182E mutation as compared to SEQ ID NO: 15. -17- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT
[0074] In some embodiments, a VSV-G protein is provided that comprises a mutation at position 199 as compared to SEQ ID NO: 16 or at position 182 as compared to SEQ ID NO: 17. SEQ ID NO: 16 is the full length protein and SEQ ID NO: 17 is the ectodomain of the VSV-G protein. The 17-mer signal peptide of MTPAFILCMLLAGSSWA (SEQ ID NO: 69) as shown at the N-terminus of SEQ ID NO: 16 is cleaved leaving a protein of SEQ ID NO: 17. Thus, although a mutation may be referred to in the context of SEQ ID NO: 17, it should be understood to also be made in the context of SEQ ID NO: 16, which contains the leader sequence, and thus would be a position number that is 17 more than the position recited for SEQ ID NO: 17. In some embodiments, the mutation inhibits or decreases the binding of the VSV-G protein to the LDL receptor (LDL-R). In some embodiments, the mutation is a V182D mutation as compared to SEQ ID NO: 17. In some embodiments, the mutation is a V182E mutation as compared to SEQ ID NO: 17.
[0075] In some embodiments, a VSV-G protein is provided that comprises a mutation at position 199 as compared to SEQ ID NO: 18 or at position 182 as compared to SEQ ID NO: 19. SEQ ID NO: 18 is the full length protein and SEQ ID NO: 19 is the ectodomain of the VSV-G protein. The 17-mer signal peptide of MNFLLLTFIVLPLCSHA (SEQ ID NO: 70) as shown at the N-terminus of SEQ ID NO: 18 is cleaved leaving a protein of SEQ ID NO: 19. Thus, although a mutation may be referred to in the context of SEQ ID NO: 19, it should be understood to also be made in the context of SEQ ID NO: 18, which contains the leader sequence, and thus would be a position number that is 17 more than the position recited for SEQ ID NO: 19. In some embodiments, the mutation inhibits or decreases the binding of the VSV-G protein to the LDL receptor (LDL-R). In some embodiments, the mutation is a V182D mutation as compared to SEQ ID NO: 19. In some embodiments, the mutation is a V182E mutation as compared to SEQ ID NO: 19.
[0076] In some embodiments, a VSV-G protein is provided that comprises a mutation at position 199 as compared to SEQ ID NO: 20 or at position 182 as compared to SEQ ID NO: 21. SEQ ID NO: 20 is the full length protein and SEQ ID NO: 21 is the ectodomain of the VSV-G protein. The 17-mer signal peptide of MLVLYLLLSLLALGAQC (SEQ ID NO: 71) as shown at the N-terminus of SEQ ID NO: 20 is cleaved leaving a protein of SEQ ID NO: 21. Thus, although a mutation may be referred to in the context of SEQ ID NO: 21, it should be understood to also be made in the context of SEQ ID NO: 20, which contains the leader sequence, and thus would be a position number that is 17 more than the position recited for SEQ ID NO: 21. In some embodiments, the mutation inhibits or decreases the binding of the VSV-G protein to the LDL receptor (LDL-R). In some embodiments, the mutation is a I182D -18- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT mutation as compared to SEQ ID NO: 21. In some embodiments, the mutation is a I182E mutation as compared to SEQ ID NO: 21.
[0077] As used herein, when a polypeptide is said to have a mutation as compared to a reference sequence, such comparison is based on an alignment such as using BlastP or ClustalW or ClutalOmega alignment software using default parameters. For example, position 182 can be found in SEQ ID NO: 2 and also as compared to the other strains as illustrated in FIG.3. FIG.3 illustrates a clustal alignment of the wild-type sequences of the ectodomains of the various strains of the VSV-G protein. The residue that is bolded and underlined are the residues that align to position 182 of SEQ ID NO: 2 of the various strains. SEQ ID NO: 2 refers to ectodomain of the VSV-G protein of the Indiana strain. SEQ ID NO: 11 refers to ectodomain of the VSV-G protein of the New Jersey strain. SEQ ID NO: 13 refers to ectodomain of the VSV-G protein of the Marraba strain. SEQ ID NO: 15 refers to ectodomain of the VSV-G protein of the Carajas strain. SEQ ID NO: 17 refers to ectodomain of the VSV- G protein of the Alagoa strain. SEQ ID NO: 19 refers to ectodomain of the VSV-G protein of the Cocal strain. SEQ ID NO: 21 refers to ectodomain of the VSV-G protein of the Morreton strain. Accordingly, the residue that aligns to residues 182 as compared to SEQ ID NO: 2 can also be mutated as provided for herein.
[0078] In some embodiments, the mutation at position 182 as compared to SEQ ID NO: 2 is not an alanine. In some embodiments, the mutation at position 182 as compared to SEQ ID NO: 2 is not a valine.
[0079] In some embodiments, the mutation at position 182 as compared to SEQ ID NO: 2 is I182S, I182H, I182T, I182Q, or I182N. In some embodiments, the mutation at position 182 as compared to SEQ ID NO: 11 is T182S, T182H, T182Q, or T182N. In some embodiments, the mutation at position 182 as compared to SEQ ID NO: 13 is A182S, A182H, A182T, A182Q, or A182N. In some embodiments, the mutation at position 182 as compared to SEQ ID NO: 15 is V182S, V182H, V182T, V182Q, or V182N. In some embodiments, the mutation at position 182 as compared to SEQ ID NO: 17 is V182S, V182H, V182T, V182Q, or V182N. In some embodiments, the mutation at position 182 as compared to SEQ ID NO: 19 is V182S, V182H, V182T, V182Q, or V182N. In some embodiments, the mutation at position 182 as compared to SEQ ID NO: 21 is I182S, I182H, I182T, I182Q, or I182N. In some embodiments, the mutation at position 182 is not a hydrophobic residue. In some embodiments, the mutation at position 182 is a charged residue. In some embodiments, the mutation at position 182 is a negatively charged residue. -19- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT
[0080] Although, the mutations may be described in reference to SEQ ID NO: 1 or SEQ ID NO: 2, which is the VSV-G protein from the Indiana strain, the mutation can also be used in other strains of the VSV-G protein. For example, the mutation can be made in the New Jersey Strain of VSV-G, the Marraba strain of VSV-G, the Carajas strain of VSV-G, the Alagoa strain of VSV-G, the Cocal strain of VSV-G, or the Morreton strain of VSV-G. In some embodiments, the sequences of each are as provided herein. Examples of these can be found, for example in U.S. Patent Application Publication No. 20200216502, which is hereby incorporated by reference. For example, the wild-type full length or ectodomain of the New Jersey Strain of VSV-G are SEQ ID NO: 10 and SEQ ID NO: 11, respectively, the wild-type full length or ectodomain of Marraba strain of VSV-G are SEQ ID NO: 12 and SEQ ID NO: 13, respectively, the wild-type full length or ectodomain of Carajas strain of VSV-G are SEQ ID NO: 14 and SEQ ID NO: 15, respectively, the wild-type full length or ectodomain of Alagoa strain of VSV-G are SEQ ID NO: 16 and SEQ ID NO: 17, respectively, the wild-type full length or ectodomain of Cocal strain of VSV-G are SEQ ID NO: 18 and SEQ ID NO: 19, respectively, or the wild-type full length or ectodomain of Morreton strain of VSV-G are SEQ ID NO: 20 and SEQ ID NO: 21, respectively.
[0081] A VSV-G protein comprising a mutation at position 182 as compared to SEQ ID NO: 2 can also comprise other mutations, such as those described in U.S. Patent Application Publication No. 20200216502, which is hereby incorporated by reference in its entirety. For example, the VSV-G protein can comprise a mutation at a position that corresponds to positions of 8, 47, 209 and / or 354 of SEQ ID NO: 2.
[0082] In some embodiments, the substitution at position 8 is by any amino acid different from the amino acid indicated at that position in the sequence SEQ ID NO: 2, except Y. In some embodiments, the substitution at position 209 is by any amino acid different from the amino acid indicated at that position in the sequence SEQ ID NO: 2, except H. In some embodiments, the substitution at position 47 is by any amino acid different from the amino acid indicated at that position in the sequence SEQ ID NO: 2, except K or R. In some embodiments, the substitution at position 354 is by any amino acid different from the amino acid indicated at that position in the sequence SEQ ID NO: 2, except K or R.
[0083] In some embodiments, the substitution is at position 47 or at position 354, or at both positions 47 and 354 are substituted by A, G, F or Q. In some embodiments, the substitution is A or Q.
[0084] In some embodiments, the substitution at position 8 is an alanine, i.e., H8A. -20- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT
[0085] In some embodiments, the substitution at position 47 is Q or N, i.e., K47Q or K47N.
[0086] In some embodiments, the protein comprises a mutation (substitution) at position 10. In some embodiments, the substitution / mutation is Q10A, Q10R, or Q10K.
[0087] In some embodiments, a protein comprising a mutation at position 182 as compared to SEQ ID NO: 2 comprises a mutation at position 182 and at least, or about, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical as compared to SEQ ID NO: 2 (or SEQ ID NO: 1 if using the full length protein). In some embodiments, the polypeptide comprises a I182D or I182E mutation. In some embodiments, the VSV-G protein comprises a I182S, I182H, I182T, I182Q, or I182N mutation.
[0088] In some embodiments, a protein comprising a mutation at position 182 as compared to SEQ ID NO: 11 comprises a mutation at position 182 and at least, or about, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical as compared to SEQ ID NO: 11 (or SEQ ID NO: 10 if using the full length protein). In some embodiments, the polypeptide comprises a T182D or T182E mutation. In some embodiments, the VSV-G protein comprises a T182S, T182H, T182Q, or T182N mutation.
[0089] In some embodiments, a protein comprising a mutation at position 182 as compared to SEQ ID NO: 13 comprises a mutation at position 182 and at least, or about, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical as compared to SEQ ID NO: 13 (or SEQ ID NO: 12 if using the full length protein). In some embodiments, the polypeptide comprises a A182D or A182E mutation. In some embodiments, the VSV-G protein comprises a A182S, A182H, A182T, A182Q, or A182N mutation.
[0090] In some embodiments, a protein comprising a mutation at position 182 as compared to SEQ ID NO: 15 comprises a mutation at position 182 and at least, or about, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical as compared to SEQ ID NO: 15 (or SEQ ID NO: 14 if using the full length protein). In some embodiments, the polypeptide comprises a V182D or V182E mutation. In some embodiments, the VSV-G protein comprises a V182S, V182H, V182T, V182Q, or V182N mutation.
[0091] In some embodiments, a protein comprising a mutation at position 182 as compared to SEQ ID NO: 17 comprises a mutation at position 182 and at least, or about, 70%, -21- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical as compared to SEQ ID NO: 17 (or SEQ ID NO: 16 if using the full length protein). In some embodiments, the polypeptide comprises a V182D or V182E mutation. In some embodiments, the VSV-G protein comprises a V182S, V182H, V182T, V182Q, or V182N mutation.
[0092] In some embodiments, a protein comprising a mutation at position 182 as compared to SEQ ID NO: 19 comprises a mutation at position 182 and at least, or about, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical as compared to SEQ ID NO: 19 (or SEQ ID NO: 18 if using the full length protein). In some embodiments, the polypeptide comprises a V182D or V182E mutation. In some embodiments, the VSV-G protein comprises a V182S, V182H, V182T, V182Q, or V182N mutation.
[0093] In some embodiments, a protein comprising a mutation at position 182 as compared to SEQ ID NO: 21 comprises a mutation at position 182 and at least, or about, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical as compared to SEQ ID NO: 21 (or SEQ ID NO: 20 if using the full length protein). In some embodiments, the polypeptide comprises a I182D or I182E mutation. In some embodiments, the VSV-G protein comprises a I182S, I182H, I182T, I182Q, or I182N mutation. Viral Particles
[0094] The mutant VSV-G proteins can be used, for example, to pseudotype a virus, such as, but not limited to a lentivirus. Accordingly, in some embodiments, a viral particle comprising a mutant VSV-G protein as provided herein are provided. In some embodiments, the viral particle comprises a VSV-G protein comprising a mutation at position 198 as compared to SEQ ID NO: 1. In some embodiments, a protein comprising a mutation at position 182 as compared to SEQ ID NO: 2 comprises a mutation at position 182 and at least, or about, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical as compared to SEQ ID NO: 2 (or SEQ ID NO: 1 if using the full length protein). In some embodiments, the polypeptide comprises a I182D or I182E mutation as compared to SEQ ID NO: 2. In some embodiments, the VSV-G protein comprises a I182S, I182H, I182T, I182Q, or I182N mutation. -22- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT
[0095] In some embodiments, the viral particle comprises a VSV-G protein comprising a mutation at position 198 as compared to SEQ ID NO: 10. In some embodiments, a protein comprising a mutation at position 182 as compared to SEQ ID NO: 11 comprises a mutation at position 182 and at least, or about, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical as compared to SEQ ID NO: 11 (or SEQ ID NO: 10 if using the full length protein). In some embodiments, the polypeptide comprises a T182D or T182E mutation as compared to SEQ ID NO: 11. In some embodiments, the VSV-G protein comprises a T182S, T182H, T182Q, or T182N mutation.
[0096] In some embodiments, the viral particle comprises a VSV-G protein comprising a mutation at position 198 as compared to SEQ ID NO: 12. In some embodiments, a protein comprising a mutation at position 182 as compared to SEQ ID NO: 13 comprises a mutation at position 182 and at least, or about, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical as compared to SEQ ID NO: 13 (or SEQ ID NO: 12 if using the full length protein). In some embodiments, the polypeptide comprises a A182D or A182E mutation as compared to SEQ ID NO: 13. In some embodiments, the VSV-G protein comprises a A182S, A182H, A182T, A182Q, or A182N mutation.
[0097] In some embodiments, the viral particle comprises a VSV-G protein comprising a mutation at position 203 as compared to SEQ ID NO: 14. In some embodiments, a protein comprising a mutation at position 182 as compared to SEQ ID NO: 15 comprises a mutation at position 182 and at least, or about, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical as compared to SEQ ID NO: 15 (or SEQ ID NO: 14 if using the full length protein). In some embodiments, the polypeptide comprises a V182D or V182E mutation as compared to SEQ ID NO: 15. In some embodiments, the VSV-G protein comprises a V182S, V182H, V182T, V182Q, or V182N mutation.
[0098] In some embodiments, the viral particle comprises a VSV-G protein comprising a mutation at position 199 as compared to SEQ ID NO: 16. In some embodiments, a protein comprising a mutation at position 182 as compared to SEQ ID NO: 17 comprises a mutation at position 182 and at least, or about, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical as compared to SEQ ID NO: 17 (or SEQ ID NO: 16 if using the full length protein). In some embodiments, the polypeptide comprises a V182D or -23- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT V182E mutation as compared to SEQ ID NO: 17. In some embodiments, the VSV-G protein comprises a V182S, V182H, V182T, V182Q, or V182N mutation.
[0099] In some embodiments, the viral particle comprises a VSV-G protein comprising a mutation at position 199 as compared to SEQ ID NO: 18. In some embodiments, a protein comprising a mutation at position 182 as compared to SEQ ID NO: 19 comprises a mutation at position 182 and at least, or about, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical as compared to SEQ ID NO: 19 (or SEQ ID NO: 18 if using the full length protein). In some embodiments, the polypeptide comprises a V182D or V182E mutation as compared to SEQ ID NO: 19. In some embodiments, the VSV-G protein comprises a V182S, V182H, V182T, V182Q, or V182N mutation.
[0100] In some embodiments, the viral particle comprises a VSV-G protein comprising a mutation at position 199 as compared to SEQ ID NO: 20. In some embodiments, a protein comprising a mutation at position 182 as compared to SEQ ID NO: 21 comprises a mutation at position 182 and at least, or about, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical as compared to SEQ ID NO: 21 (or SEQ ID NO: 20 if using the full length protein). In some embodiments, the polypeptide comprises a I182D or I182E mutation as compared to SEQ ID NO: 21. In some embodiments, the VSV- G protein comprises a I182S, I182H, I182T, I182Q, or I182N mutation.
[0101] In some embodiments, the VSV-G protein further comprises a mutation at position that corresponds to positions 214 and / or 352 of SEQ ID NO: 2. In some embodiments, the residue that corresponds to position 214 of SEQ ID NO: 2 is T214. In some embodiments, the residue that corresponds to position 352 of SEQ ID NO: is T352. In some embodiments, the VSV-G protein comprises mutation that corresponds to T214N mutation as compared to SEQ ID NO: 2. In some embodiments, the VSV-G protein comprises mutation that corresponds to T352A mutation as compared to SEQ ID NO: 2. In some embodiments, the VSV-G protein comprises a T214N and T352A mutations as compared to SEQ ID NO: 2. These mutations can be combined with any other mutations as provided for herein. In some embodiments, the T214N and / or T352A mutations are combined with the I182E or I182D mutations. In some embodiments, a VSV-G protein comprises an amino acid sequence of SEQ ID NO: 22 and SEQ ID NO: 23, which combines the I182D or I182E, respectively, with the T214N and T352A mutations. The sequences are also illustrated below with the leader sequences, which are removed during protein processing. -24- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT VSV-G Protein_ I196D, T230N and T368A mutations (with leader sequence and adjusted numbering) MKCLLYLAFLFIGVNCKFTIVFPHNQKGNWKNVPSNYHYCPS SSDLNWHNDLIGTALQVKMPKSHKAIQADGWMCHASKWVTTC DFRWYGPKYITHSIRSFTPSVEQCKESIEQTKQGTWLNPGFP PQSCGYATVTDAEAVIVQVTPHHVLVDEYTGEWVDSQFINGK CSNYICPTVHNSTTWHSDYKVKGLCDSNLDSMDITFFSEDGE LSSLGKEGTGFRSNYFAYENGGKACKMQYCKHWGVRLPSGVW FEMADKDLFAAARFPECPEGSSISAPSQTSVDVSLIQDVERI LDYSLCQETWSKIRAGLPISPVDLSYLAPKNPGTGPAFTIIN GTLKYFETRYIRVDIAAPILSRMVGMISGTTAERELWDDWAP YEDVEIGPNGVLRTSSGYKFPLYMIGHGMLDSDLHLSSKAQV FEHPHIQDAASQLPDDESLFFGDTGLSKNPIELVEGWFSSWK SSIASFFFIIGLIIGLFLVLRVGIHLCIKLKHTKKRQIYTDI EMNRLGK (SEQ ID NO: 24) VSV-G Protein_I182D, T214N and T352A mutations (without leader sequence) KFTIVFPHNQKGNWKNVPSNYHYCPSSSDLNWHNDLIGTALQ VKMPKSHKAIQADGWMCHASKWVTTCDFRWYGPKYITHSIRS FTPSVEQCKESIEQTKQGTWLNPGFPPQSCGYATVTDAEAVI VQVTPHHVLVDEYTGEWVDSQFINGKCSNYICPTVHNSTTWH SDYKVKGLCDSNLDSMDITFFSEDGELSSLGKEGTGFRSNYF AYENGGKACKMQYCKHWGVRLPSGVWFEMADKDLFAAARFPE CPEGSSISAPSQTSVDVSLIQDVERILDYSLCQETWSKIRAG LPISPVDLSYLAPKNPGTGPAFTIINGTLKYFETRYIRVDIA APILSRMVGMISGTTAERELWDDWAPYEDVEIGPNGVLRTSS GYKFPLYMIGHGMLDSDLHLSSKAQVFEHPHIQDAASQLPDD ESLFFGDTGLSKNPIELVEGWFSSWKSSIASFFFIIGLIIGL FLVLRVGIHLCIKLKHTKKRQIYTDIEMNRLGK (SEQ ID NO: 22) VSV-G Protein with I196E, T230N and T368A mutations (with leader sequence and adjusted numbering) MKCLLYLAFLFIGVNCKFTIVFPHNQKGNWKNVPSNYHYCPS SSDLNWHNDLIGTALQVKMPKSHKAIQADGWMCHASKWVTTC DFRWYGPKYITHSIRSFTPSVEQCKESIEQTKQGTWLNPGFP PQSCGYATVTDAEAVIVQVTPHHVLVDEYTGEWVDSQFINGK CSNYICPTVHNSTTWHSDYKVKGLCDSNLESMDITFFSEDGE LSSLGKEGTGFRSNYFAYENGGKACKMQYCKHWGVRLPSGVW FEMADKDLFAAARFPECPEGSSISAPSQTSVDVSLIQDVERI LDYSLCQETWSKIRAGLPISPVDLSYLAPKNPGTGPAFTIIN GTLKYFETRYIRVDIAAPILSRMVGMISGTTAERELWDDWAP YEDVEIGPNGVLRTSSGYKFPLYMIGHGMLDSDLHLSSKAQV FEHPHIQDAASQLPDDESLFFGDTGLSKNPIELVEGWFSSWK SSIASFFFIIGLIIGLFLVLRVGIHLCIKLKHTKKRQIYTDI EMNRLGK (SEQ ID NO: 25) -25- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT VSV-G Protein with I182E, T214N and T352A mutations (without leader sequences) KFTIVFPHNQKGNWKNVPSNYHYCPSSSDLNWHNDLIGTALQ VKMPKSHKAIQADGWMCHASKWVTTCDFRWYGPKYITHSIRS FTPSVEQCKESIEQTKQGTWLNPGFPPQSCGYATVTDAEAVI VQVTPHHVLVDEYTGEWVDSQFINGKCSNYICPTVHNSTTWH SDYKVKGLCDSNLESMDITFFSEDGELSSLGKEGTGFRSNYF AYENGGKACKMQYCKHWGVRLPSGVWFEMADKDLFAAARFPE CPEGSSISAPSQTSVDVSLIQDVERILDYSLCQETWSKIRAG LPISPVDLSYLAPKNPGTGPAFTIINGTLKYFETRYIRVDIA APILSRMVGMISGTTAERELWDDWAPYEDVEIGPNGVLRTSS GYKFPLYMIGHGMLDSDLHLSSKAQVFEHPHIQDAASQLPDD ESLFFGDTGLSKNPIELVEGWFSSWKSSIASFFFIIGLIIGL FLVLRVGIHLCIKLKHTKKRQIYTDIEMNRLGK (SEQ ID NO: 23)
[0102] In some embodiments, the VSV-G protein comprising a mutation at position 182 as compared to SEQ ID NO: 2 further comprises a mutation at position that corresponds to positions 38 and / or 320 or SEQ ID NO: 2. In some embodiments, the residue that corresponds to position 38 of SEQ ID NO: 2 is T38. In some embodiments, the residue that corresponds to position 320 of SEQ ID NO: 2 is T320. In some embodiments, the VSV- G protein comprises mutation that corresponds to T38A mutation as compared to SEQ ID NO: 2. In some embodiments, the VSV-G protein comprises mutation that corresponds to T320A mutation as compared to SEQ ID NO: 2. In some embodiments, the VSV-G protein comprises a T38A and T320A mutations as compared to SEQ ID NO: 2. These mutations can be combined with any other mutations as provided for herein.
[0103] In some embodiments, the other strains of the VSV-G protein as described herein can further comprise one or more mutations corresponding to any of the other mutations as compared to SEQ ID NO: 2 and as provided for herein. For example, the other strains of the VSV-G protein as described herein can also comprises the mutations that correspond to T38A, T214N, T320A, and / or T352A in SEQ ID NO: 2. In some embodiments, the other strains of the VSV-G protein as described herein can also comprises the mutations that correspond to T214N and / or T352A in SEQ ID NO: 2 and as illustrated in SEQ ID NO: 22 and SEQ ID NO: 23.
[0104] In some embodiments, the composition comprises a mutation as described in Hwang et al., Gene Ther 2013 Aug;20(8):807-15. (Epub 2013 Jan 31), which is hereby incorporated by reference in its entirety. For example, the mutations can be. at positions 230, 368, 66, and / or 162 that corresponds to SEQ ID NO: 1. The positions will be 16 positions less as compared to SEQ ID NO: 2, when the leader sequence is removed. In some embodiments, the mutations at those positions are, for example, T230N, T368A, K66T, S162T, -26- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT or any combination thereof. In some embodiments, the VSV-G protein comprises a T230N and a T368A mutation. In some embodiments, the VSV-G polypeptide comprises a K66T, S162T, T230N, and a T368A. These positions are those that correspond to the positions in the full length protein (SEQ ID NO: 1). In some embodiments, the VSV-G protein comprises T230N mutation, a T368A mutation, a K66T mutation, a S162T mutation, or any combination thereof. In some embodiments, the VSV-G protein further comprises one or more mutations in addition to the mutation that corresponds to position 182 of SEQ ID NO: 2, such as those described in U.S. Patent Application Publication No. 20200216502, which is hereby incorporated by reference in its entirety. For example, the VSV-G protein can further comprise a mutation at a position that corresponds to positions of 8, 47, 209 and / or 354 of SEQ ID NO: 2.
[0105] In some embodiments, the substitution at position 8 is by any amino acid different from the amino acid indicated at that position in the sequence SEQ ID NO: 2, except Y. In some embodiments, the substitution at position 209 is by any amino acid different from the amino acid indicated at that position in the sequence SEQ ID NO: 2, except H. In some embodiments, the substitution at position 47 is by any amino acid different from the amino acid indicated at that position in the sequence SEQ ID NO: 2, except K or R. In some embodiments, the substitution at position 354 is by any amino acid different from the amino acid indicated at that position in the sequence SEQ ID NO: 2, except K or R. In some embodiments, the substitution is at position 47 or at position 354, or at both positions 47 and 354 are substituted by A, G, F or Q. In some embodiments, the substitution is A or Q. In some embodiments, the substitution at position 8 is an alanine, i.e., H8A. In some embodiments, the substitution at position 47 is Q or N, i.e., K47Q or K47N. In some embodiments, the protein comprises a mutation (substitution) at position 10. In some embodiments, the substitution / mutation is Q10A, Q10R, or Q10K.
[0106] Additional or alternative VSV-G proteins and modified VSV-G proteins (i.e. those containing at least one mutation as compared to the parent strain) are known and any such VSV-G protein is within the scope of the present disclosure. Suitable examples of additional VSV-G proteins and modified VSV-G proteins may be found at least in WO2022 / 183072, WO2024 / 145593, WO2024 / 145599, WO2024 / 145605, WO2024 / 145622, WO2025 / 003526, US 2024 / 0150788 and US 2024 / 0218390, each of which are incorporated by reference in their entirety.
[0107] Additionally, in some embodiments, instead of the VSV-G protein or mutant thereof, the viruses can be pseudotyped with other viral structural proteins. Suitable -27- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT examples of alternate viral structural proteins may be found at least in WO2023 / 064884, WO2023 / 114698, WO2023 / 114884, and WO2023 / 154858, each of which are incorporated by reference in their entirety. Targeting Moieties
[0108] In some embodiments, the viral particle comprises a targeting moiety. The targeting moiety can be used to target the viral particle comprising the mutant VSV-G protein to a cell that expresses the target to which the targeting moiety binds to. In some embodiments, the targeting moiety is an antibody, a scFv antibody, an antigen binding domain, an ankyrin repeat (e.g., DARPIN), a VHH domain antibody, a nanobody, single domain antibody, a FN3 domain, or any combination thereof. The targeting moiety can be attached to the viral surface through an IgG Fc stalk. In some embodiments, the stalk comprises a transmembrane domain. In some embodiments, the transmembrane domain comprises the CD28 transmembrane domain. In some embodiments, the targeting moiety is attached (fused or linked) an envelope glycoprotein G or H of a virus of the Paramyxoviridae family, such as a morbillivirus, such as Measles virus, or a henipavirus, such as Nipah virus, Cedar virus, or Hendra virus. In some embodiments, the targeting moiety can be attached (fused or linked) to a glycoprotein of a virus of the Rhabdoviridae family, such as a vesicular stomatitis New Jersey virus, a vesicular stomatitis Indiana virus, a vesicular stomatitis Alagoas virus, a vesicular stomatitis Maraba virus, a vesicular stomatitis Carajas virus, Parainfluenza virus, Spodoptera frugiperda rhabdovirus isolate Sf G, Drosophila obscura sigmavirus 10A, Wuhan insect virus 7, Perch virus, or Spring viremia of carp virus. In some embodiments, the VSV protein is the mutated proteins, such as those provided for herein. In some embodiments, the targeting moiety is attached to a glycoprotein of a virus of the Filoviridae family, such as Ebola virus or a glycoprotein of a virus of the Arenaviridae family, such as Machupo virus.
[0109] In some embodiments, the targeting moiety is a scFv. In some embodiments, the targeting moiety is a single domain antibody. In some embodiments, the targeting moiety is a VHH.
[0110] In some embodiments, the targeting moiety binds to CD7, CD8, cKit (CD117), CD4, CD3, CD5, CD6, CD2, TCR alpha, TCR beta, TCR gamma, TCR delta, CD10, CD34, CD110, CD33, CD14, CD68, CCR7, CD62L, CD25, CCR2, CCR3, CCR4, CCR5, CCR6, CCR7, or CXCR3, A glycosylated CD43 epitope expressed on acute leukemia or lymphoma but not on hematopoietic progenitors; A glycosylated CD43 epitope expressed on non-hematopoietic cancers; A kinase anchor protein 4 (AKAP-4); Adrenoceptor beta 3 -28- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT (ADRB3); AFP; Anaplastic lymphoma kinase (ALK); Androgen receptor; Angiopoietin- binding cell surface receptor 2 (Tie 2); Auto antibody to desmoglein 1 (Dsgl); Auto antibody to desmoglein 3 (Dsg3); B7H3 (CD276); Biotin; Bone marrow stromal cell antigen 2 (BST2); BST1 / CD157; Cancer / testis antigen 1 (NY-ESO-1); Cancer / testis antigen 2 (LAGE-la); Carbonic anhydrase IX (CA1X); Carcinoembryonic antigen (CEA); CCCTC-Binding Factor (Zinc Finger Protein)-Like (BORIS or Brother of the Regulator of lmprinted Sites); CCR4; CD5; CD19; CD20; CD22; CD24; CD30; CD32 (FCGR2A); CD33; CD34; CD38; CD44v6; CD72; CD79a; CD79b; CD97; CD99; CD123; CD171; CD179a; CD179b-IGLll; CD200R; CD276 / B7H3; CD300 molecule-like family member f (CD300LF); CDH1-CD324; CDH6; CDH17; CDH19; Chromosome X open reading frame 61 (CXORF61); Claudin 6 (CLDN6); Claudinl8.2 (CLD18A2 or CLDN18A.2); CMV pp65; C-MYC epitope Tag; Cripto; CS1 (also referred to as CD2 subset 1 or CRACC or SLAMF7 or CD319 or 19A24); CSF2RA (GM- CSFR-alpha); C-type lectin domain family 12 member A (CLEC12A); C-type lectin-like molecule-1 (CLL-1 or CLECL1); Cyclin Bl; Cytochrome P450 IB 1 (CYP1B 1); DLL3; EBV- EBNA3c; EGF-bke module- containing mucin-like hormone receptor-like 2 (EMR2); Elongation factor 2 mutated (ELF2M); Ephrin B2; Ephrin type-A receptor 2 (EphA2); Epidermal growth factor receptor (EGFR); Epidermal growth factor receptor variant III (EGFRviii); Epithelial cell adhesion molecule (EPCAM); ERG; ETS translocation-variant gene 6 located on chromosome 12p (ETV6-AML); Fc fragment of IgA receptor (FCAR or CD89); Fc receptor-like 5 (FCRL5); Fibroblast activation protein alpha (FAP); FITC; Fms Like Tyrosine Kinase 3 (FLT3); Folate receptor alpha (FRa or FR1); Folate receptor beta (FRb); Follicle stimulating hormone receptor (FSHR); Fos-related antigen 1; Fucosyl-GMl; G protein coupled receptor class C group 5 member D (GPRC5D); G protein-coupled receptor 20 (GPR20); GAD; Ganglioside G2 (GD2) ; Ganglioside GD3 (aNeu5Ac(2-8)aNeu5Ac(2- 3)bDGalp(l-4 )bDGlcp(l-l)Cer); Ganglioside GM3 (aNeu5Ac(2-3)bDClalp(l- 4)bDGlcp(l- l)Cer); GD3; GFRalpha4; Glycoprotein 100 (gplOO); Glypican-3 (GPC3); Gonadotropin Hormone receptor (CGHR or GR); GpA33; GpNMB; GPRC5D; Guanylyl cyclase C (GCC); Heat shock protein 70-2 mutated (mut hsp70-2); Hepatitis A virus cellular receptor 1 (HAVCR1); Hexasaccharide portion of globoH glycoceramide (GloboH); High molecular weight-melanoma associated antigen (HMWMAA); HIV1 envelope glycoprotein; HLA; HLA- DOA; HLA-A; HLA-A2; HLA-B; HLA-C; HLA-DM; HLA-DOB; HLA-DP; HLA-DQ; HLA- DR; HLA-G; HTLVl-Tax; Human papilloma virus E6 (HPV E6); Human papilloma virus E7 (HPV E7); Human Telomerase reverse transcriptase (hTERT); IgE; IL13Ra2; ILl lRa; Immunoglobulin lambda-like polypeptide 1 (IGLL1); Influenza A hemagglutinin (HA); -29- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT Insulin-like growth factor 1 receptor (IGF-I receptor); Interleukin 11 receptor alpha (IL-llRa); Interleukin- 13 receptor subunit alpha-2 (IL-13Ra2 or CD213A2); Intestinal carboxyl esterase; KIT (CD117); KSHV K8.1; KSHV-gH; LAMP1 ; Legumain; Leukocyte immunoglobulin-like receptor subfamily A member 2 (LILRA2); Leukocyte-associated immunoglobulin-like receptor 1 (LAIR1); Leutenizing hormone receptor (LHR); Lewis(Y) antigen; Lews Ag; Livl; Locus K 9 (LY6K); Low conductance chloride channel; Lymphocyte antigen 6 complex; Lymphocyte antigen 75 (LY75); Lymphocyte-specific protein tyrosine kinase (LCK); Mammary gland differentiation antigen (NY-BR-1); Melanoma antigen recognized by T cells 1 (MelanA or MARTI); Melanoma- associated antigen 1 (MAGE-A1); Melanoma cancer testis antigen-1 (MAD-CT-1); Melanoma cancer testis antigen-2 (MAD-CT-2); Melanoma inhibitor of apoptosis (ML-IAP); Mesothelin; MPL; Mucin 1 cell surface associated (MUC1); N-Acetyl glucosaminyl-transferase V (NA17); Nectin-4; Neural cell adhesion molecule (NCAM); NKG2D; NYBR1; O-acetyl-GD2 ganglioside (OAcGD2); Olfactory receptor 51E2 (OR51E2); Oncogene fusion protein consisting of breakpoint cluster region (BCR) and Abelson murine leukemia viral oncogene homolog 1 (Abl) (bcr-abl); P53 mutant; Paired box protein Pax-3 (PAX3); Paired box protein Pax-5 (PAX5); Pannexin 3 (PANX3); PDL1; P-glycoprotein; Placenta-specific 1 (PLAC1); Platelet-derived growth factor receptor beta (PDGFR-beta); Polysialic acid; Proacrosin binding protein sp32 (OY-TES1); Prostase; Prostate carcinoma tumor antigen-1 (PCT A-l or Galectin 8); Prostate stem cell antigen (PSCA); Prostate-specific membrane antigen (PSMA); Prostatic acid phosphatase (PAP); Prostein; Protease Serine 21 (Testisin or PRSS21); Proteasome (Prosome Macropain) Subunit Beta Type 9 (LMP2); PTK7; Ras G12V; Ras Homolog Family Member C (RhoC); Rat sarcoma (Ras) mutant; Receptor for Advanced Gly cation Endproducts (RAGE-1); Receptor tyrosine kinase-like orphan receptor 1 (ROR1); Receptor tyrosine-protein kinase ERBB2 or Her-22 / neu; Renal ubiquitous 1 (RU1); Renal ubiquitous 2 (RU2); Sarcoma translocation breakpoints; Serine 2 (TMPRSS2) ETS fusion gene; Sialyl Lewis adhesion molecule (sLe); SLAMF4; SLAMF6; Slea (CA19.9 or Sialyl Lewis Antigen); Sperm protein 17 (SPA17); Squamous Cell Carcinoma Antigen Recognized By T Cells 3 (SART3); Stage-specific embryonic antigen-4 (SSEA-4); STEAP1; Survivin; Synovial sarcoma X breakpoint 2 (SSX2); TCR Gamma Alternate Reading Frame Protein (TARP); TCR-beta1 chain; TCR-beta2 chain; TCR-delta chain; TCR-gamma chain; TCRgamma-delta; Telomerase; TGFbetaR2; The antigen recognized by TNT antibody; Thyroid stimulating hormone receptor (TSHR); Timl- / HVCR1; Tissue Factor 1 (TF1); Tn ag; Tn antigen ((Tn Ag) or (GalNAca-Ser / Thr)); TNF receptor family member B cell maturation (BCMA); Transglutaminase 5 (TGS5); Transmembrane protease; TROP2; Tumor endothelial -30- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT marker 1 (TEM1 / CD248); Tumor endothelial marker 7-related (TEM7R); Tumor protein p53 (p53); Tumor-associated glycoprotein 72 (TAG72); Tyrosinase; Tyrosinase-related protein 2 (TRP-2); Uroplakin 2 (UPK2); Vascular endothelial growth factor receptor 2 (VEGFR2); V- myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog (MYCN); Wilms tumor protein (WT1); or X Antigen Family Member 1A (XAGE1). In some embodiments, the targeting moiety binds to CD7. In some embodiments, the targeting moiety binds to CD8.
[0111] In some embodiments, the targeting moiety binds to a target that is present on a cell, such as an immune cell. In some embodiments, the cell is an immune cell, such as, but not limited to, T cell, B cell; NK cell, dendritic cell, neutrophils, macrophages, a cancer cell; or, for example, CD3+ T cell; CD4+ T cell; CD7+ T cell, CD8+ T cell; CD19+ B cell; CD19+ cancer cell; CD20+ B cell; CD20+ cancer cell; CD30+ lung epithelial cell; CD34+ haematopoietic stem cell; CD105+ endothelial cell; CD105+ haematopoietic stem cell; CD117+ haematopoietic stem cell; CD133+ cancer cell; EpCAM+ cancer cell; GluA2+ neuron; GluA4+ neuron; Haematopoietic stem cell; Hepatocyte; Her2 / Neu+ cancer cell; NKG2D+ natural killer cell; SLC1A3+ astrocyte; SLC7A10+ adipocyte. In some embodiments, the cell is a T cell. In some embodiments, the cell is a B cell. In some embodiments, the cell is a CD7+ T cell and / or CD8+ T cell.
[0112] In some embodiments, the targeting moiety (a polypeptide) can bind to CD7.
[0113] In some embodiments, the polypeptide binds to CD7. In some embodiments, the polypeptide that binds to CD7 is an antibody which binds to non-human primate CD7. In some embodiments, the polypeptide that binds to CD7 is an antibody which binds to human CD7. The sequence of human CD7 (UniProtKB P09564) is as follows (SEQ ID NO: 29): MAGPPRLLLLPLLLALARGLPGALAAQEVQQSPHCTTVPVGASVNITCSTSGGLRGI YLRQLGPQPQDIIYYEDGVVPTTDRRFRGRIDFSGSQDNLTITMHRLQLSDTGTYTC QAITEVNVYGSGTLVLVTEEQSQGWHRCSDAPPRASALPAPPTGSALPDPQTASALP DPPAASALPAALAVISFLLGLGLGVACVLARTQIKKLCSWRDKNSAACVVYEDMSHS RCNTLSSPNQYQ (SEQ ID NO: 29)
[0114] In some embodiments, the CD7 antibody comprises a Fc region. The Fc region can be linked to the heavy or light chain of the antibody. The Fc region may be fused directly to the heavy or light chain of the antibody or may be fused indirectly to the heavy or light chain of the antibody via, for example, a peptide linker as provided for herein. In some embodiments, the Fc region is an IgG Fc. In some embodiments, the IgG is selected from IgG1, -31- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT IgG2, IgG3, or IgG4. In some embodiments, the IgG Fc is IgG1 Fc. In some embodiments, the antibody comprises an Fc constant region of SEQ ID NO: 26 as set forth below: ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPA PELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAK TKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPRE PQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDG SFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK (SEQ ID NO: 26)
[0115] In some embodiments, the IgG fc is IgG2 Fc. In some embodiments, the antibody comprises an Fc constant region of SEQ ID NO: 27 as set forth below: STKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ SSGLYSLSSVVTVPSSSLGTQTYTCNVDHKPSNTKVDKTVERKCCVECPPCPAPPVA GPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVQFNWYVDGVEVHNAKTKPRE EQFNSTFRVVSVLTVVHQDWLNGKEYKCKVSNKGLPAPIEKTISKTKGQPREPQVYT LPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPMLDSDGSFFLY SKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK (SEQ ID NO: 27)
[0116] In some embodiments, the IgG fc is IgG4 Fc. In some embodiments, the antibody comprises an Fc constant region of SEQ ID NO: 28 as set forth below: STKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ SSGLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVESKYGPPCPSCPAPEFL GGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSQEDPEVQFNWYVDGVEVHNAKTKPR EEQFNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKGLPSSIEKTISKAKGQPREPQVY TLPPSQEEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFL YSRLTVDKSRWQEGNVFSCSVMHEALHNHYTQKSLSLSLGK (SEQ ID NO: 28)
[0117] In some embodiments, the IgG Fc is a variant of an IgG1 Fc protein (SEQ ID NO: 26). In some embodiments, the variant IgG1 Fc protein comprises one or more of the mutations that corresponds to those selected from the group consisting of: L234A, L235A, N297A, P329G, I253A, H310A, and H435A of SEQ ID NO: 26. Any of the mutations L234A, L235A, N297A, P329G, I253A, H310A, and H435A of SEQ ID NO: 26 may be present or absent and the mutations may be combined in any combination. In some embodiments, the variant IgG1 Fc protein comprises a mutation that corresponds to L234A and L235A of SEQ ID NO: 26. In some embodiments, the variant IgG1 Fc protein comprises a mutation that corresponds to N297A of SEQ ID NO: 26. In some embodiments, the variant IgG1 Fc protein comprises a mutation that corresponds to P329G of SEQ ID NO: 26. In some embodiments, the variant IgG1 Fc protein comprises a mutation that corresponds to L234A, L235A, N297A, and P329G of SEQ ID N: 83. In some embodiments, the variant IgG1 Fc -32- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT protein comprises a mutation that corresponds to I253A of SEQ ID NO: 26. In some embodiments, the variant IgG1 Fc protein comprises a mutation that corresponds to H310A of SEQ ID NO: 26. In some embodiments, the variant IgG1 Fc protein comprises a mutation that corresponds to H435A of SEQ ID NO: 26. In some embodiments, the variant IgG1 Fc protein comprises a mutation that corresponds to I253A, H310A, and H435A of SEQ ID NO: 26.
[0118] In some embodiments, the IgG Fc is a variant of an IgG2 Fc protein (SEQ ID NO: 27). In some embodiments, the variant IgG2 Fc protein comprises one or more mutations selected from the group consisting of: N297A, P329G, I253A, H310A, and H435A as those position correspond to SEQ ID NO: 27. Any of the mutations N297A, P329G, I253A, H310A, and H435A of SEQ ID NO: 27 may be present or absent and the mutations may be combined in any combination. In some embodiments, the variant IgG2 Fc protein comprises a mutation that corresponds to N297A of SEQ ID NO: 27. In some embodiments, the variant IgG2 Fc protein comprises a mutation that corresponds to P329G of SEQ ID NO: 27. In some embodiments, the variant IgG2 Fc protein comprises a mutation that corresponds to N297A and P329G of SEQ ID NO: 27. In some embodiments, the variant IgG2 Fc protein comprises a mutation that corresponds to I253A of SEQ ID NO: 27. In some embodiments, the variant IgG2 Fc protein comprises a mutation that corresponds to H310A of SEQ ID NO: 27. In some embodiments, the variant IgG2 Fc protein comprises a mutation that corresponds to H435A of SEQ ID NO: 27. In some embodiments, the variant IgG2 Fc protein comprises a mutation that corresponds to I253A, H310A, and H435A of SEQ ID NO: 27.
[0119] In some embodiments, the IgG Fc protein is a variant of an IgG4 Fc protein (SEQ ID NO: 28). In some embodiments, the variant IgG4 Fc protein comprises one or more mutations selected from the group consisting of: S228P, L235E, N297A, P329G, I253A, H310A, and H435A as those positions correspond to SEQ ID NO: 28. Any of the mutations S228P, L235E, N297A, P329G, I253A, H310A, and H435A of SEQ ID NO: 28 may be present or absent and the mutations may be combined in any combination. In some embodiments, the variant IgG4 Fc protein comprises a mutation that corresponds to S228P of SEQ ID NO: 28. In some embodiments, the variant IgG4 Fc protein comprises a mutation that corresponds to L235E of SEQ ID NO: 28. In some embodiments, the variant IgG4 Fc protein comprises a mutation that corresponds to N297A of SEQ ID NO: 28. In some embodiments, the variant IgG4 Fc protein comprises a mutation that corresponds to P329G of SEQ ID NO: 28. In some embodiments, the variant IgG4 Fc protein comprises a mutation that corresponds to S228P, L235E, N297A, and P329G of SEQ ID NO: 28. In some embodiments, the variant IgG4 Fc protein comprises a mutation that corresponds to I253A of SEQ ID NO: 28. In some -33- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT embodiments, the variant IgG4 Fc protein comprises a mutation that corresponds to H310A of SEQ ID NO: 28. In some embodiments, the variant IgG4 Fc protein comprises a mutation that corresponds to H435A of SEQ ID NO: 28. In some embodiments, the variant IgG4 Fc protein comprises a mutation that corresponds to I253A, H310A, and H435A of SEQ ID NO: 28.
[0120] In some embodiments, the Fc region comprises a variant Fc polypeptide. In some embodiments, the variant Fc polypeptide is a variant Fc polypeptide as provided for in PCT Publication No. WO2024026284 which is hereby incorporated by reference in its entirety. In some embodiments, the variant Fc polypeptide comprises an amino acid sequence that is at least 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to the amino acid sequence of SEQ ID NO: 82: EPKSCDKTHTCPPCPAPEAAGGPSVFLFPPKPKDTLMASRTPEVTCVVVDVS HEDPEVKFNWYVDGVEVHNAKTKPREEQYASTYRVVSVLTVLAQDWLNGKEY KCKVSNKALGAPIEKTISKAKGQPREPQVYTLPPSRDELTKNQVSLTCLVKG FYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVF SCSVMHEALHNAYTQKSLSLSPGK (SEQ ID NO: 82) In some embodiments, the variant Fc polypeptide comprises an amino acid sequence of SEQ ID NO: 82.
[0121] In some embodiments, the targeting moiety binds to CD7 and comprises an HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, LCDR3, VH, and VL as recited in Table 1 and Table 2 below: Table 1 - CD7 targeting moiety CD7AB1 CDR sequences Numbering HCDR1 HCDR2 HCDR3 LCDR1 LCDR2 LCDR3 System P QSEQ ID NO: AB ID NO: Region Sequence 42 CD7AB1 VHQVQLQQPGAELVKPGASVKLSCKASGYPFTSYWIHWVKQRPGRGLEWLGRIDPNSGDTKYNEKFKNKATLTVDKSSTTAYMQLSSLTSEDSAVYYC ARSPYYSNDNSMDYWGQGTSVTVSSDOCKET NO: INH-032WO PATENT I T
[0122] The VH and the VL sequences can be in any format, including, but not limited to an scFv format where the VH and VL regions are linked with a peptide linker. Examples of peptide linkers that can be used to link various peptides provided for herein include, but are not limited to: (GGGGS)n (SEQ ID NO: 64), wherein each n is independently 1-4. In some embodiments, n is 1. In some embodiments, n is 2. In some embodiments, n is 3. In some embodiments, n is 4. In some embodiments, the variable regions are not linked with a peptide linker. In some embodiments, the polypeptide comprises SEQ ID NO: 42 and SEQ ID NO: 43. In some embodiments, the targeting moiety comprises a linked peptide represented by a formula of VL-Z-VH, wherein Z is a peptide linker. In some embodiments, the targeting moiety comprises a heavy chain variable region as set forth in SEQ ID NO: 42 linked via a linker sequence GGGGSGGGGSGGGGSGGGGS (SEQ ID NO: 72) to a light chain variable region as set forth in SEQ ID NO: 43. In some embodiments, a targeting moiety comprising a VL linked via a peptide linker to a VH has the sequence as set forth below: DILLTQSPAILSVSPGERVSFSCRASQSIGTSIHWYQQRTNDSPRLLIKYASESISG IPSRFSGSGSGTDFTLSINSVESEDIADYYCQQSNSWPTTFGGGTKLEIKRGGGGSG GGGSGGGGSGGGGSQVQLQQPGAELVKPGASVKLSCKASGYPFTSYWIHWVKQRPGR GLEWLGRIDPNSGDTKYNEKFKNKATLTVDKSSTTAYMQLSSLTSEDSAVYYCARSP YYSNDNSMDYWGQGTSVTVSS (SEQ ID NO: 44)
[0123] In some embodiments, the targeting moiety comprises a linked peptide represented by a formula of VH-Z-VL, wherein Z is a peptide linker. In some embodiments, the targeting moiety comprises a heavy chain variable region as set forth in SEQ ID NO: 42 linked via a linker sequence GGGGSGGGGSGGGGSGGGGS (SEQ ID NO: 72) to a light chain variable region as set forth in SEQ ID NO: 43. In some embodiments, a targeting moiety comprising a VH linked via a peptide linker to a VL has the sequence as set forth below: QVQLQQPGAELVKPGASVKLSCKASGYPFTSYWIHWVKQRPGRGLEWLGRIDPNSGD TKYNEKFKNKATLTVDKSSTTAYMQLSSLTSEDSAVYYCARSPYYSNDNSMDYWGQG TSVTVSSGGGGSGGGGSGGGGSGGGGSDILLTQSPAILSVSPGERVSFSCRASQSIG TSIHWYQQRTNDSPRLLIKYASESISGIPSRFSGSGSGTDFTLSINSVESEDIADYY CQQSNSWPTTFGGGTKLEIKR (SEQ ID NO: 45)
[0124] In some embodiments, the targeting moiety (a polypeptide) can bind to CD8. -35- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT
[0125] In some embodiments, the polypeptide binds to CD8. In some embodiments, the polypeptide binds to CD8-alpha. In some embodiments, the polypeptide binds to CD8-beta. In some embodiments, the polypeptide binds to CD8 heterodimer. In some embodiments, the CD8 heterodimer comprises CD8-alpha and CD8-beta subunits. In some embodiments, the polypeptide binds to CD8-alpha homodimer. In some embodiments, the polypeptide that binds to CD8 is an antibody which binds to non-human primate CD8. In some embodiments, the antibody that binds to non-human primate CD8 is an antibody which binds to non-human primate CD8-alpha. In some embodiments, the antibody that binds to non-human primate CD8 is an antibody which binds to non-human primate CD8-beta. In some embodiments, the antibody that binds to non-human primate CD8 is an antibody which binds to non-human primate CD8-alpha homodimer. In some embodiments, the antibody that binds to non-human primate CD8 is an antibody which binds to non-human primate CD8 heterodimer. In some embodiments, the polypeptide that binds to CD8 is an antibody which binds to human CD8. In some embodiments, the antibody that binds to human CD8 is an antibody which binds to human CD8-alpha. In some embodiments, the antibody that binds to human CD8 is an antibody which binds to human CD8-beta. In some embodiments, the antibody that binds to human CD8 is an antibody which binds to human CD8-alpha homodimer. In some embodiments, the antibody that binds to human CD8 is an antibody which binds to human CD8 heterodimer. The sequence of human CD8-alpha (UniProtKB Q8TAW8) is as follows (SEQ ID NO: 46): MALPVTALLLPLALLLHAARPSQFRVSPLDRTWNLGETVELKCQVLLSNPTSGCSWL FQPRGAAASPTFLLYLSQNKPKAAEGLDTQRFSGKRLGDTFVLTLSDFRRENEGCYF CSALSNSIMYFSHFVPVFLPAKPTTTPAPRPPTPAPTIASQPLSLRPEACRPAAGGA VHTRGLDFACDIYIWAPLAGTCGVLLLSLVITLYCNHRNRRRVCKCPRPVVKSGDKP SLSARYV (SEQ ID NO: 46)
[0126] The sequence of human CD8-beta (UniProtKB Q8TD28) is as follows (SEQ ID NO: 47): MRPRLWLLLAAQLTVLHGNSVLQQTPAYIKVQTNKMVMLSCEAKISLSNMRIYWLRQ RQAPSSDSHHEFLALWDSAKGTIHGEEVEQEKIAVFRDASRFILNLTSVKPEDSGIY FCMIVGSPELTFGKGTQLSVVDFLPTTAQPTKKSTLKKRVCRLPRPETQKGPLCSPI TLGLLVAGVLVLLVSLGVAIHLCCRRRRARLRFMKQLYK (SEQ ID NO: 47)
[0127] In some embodiments, the CD8 antibody comprises a Fc region. The Fc region can be linked to the heavy or light chain of the antibody. The Fc region may be fused directly to the heavy or light chain of the antibody or may be fused indirectly to the heavy or light chain of the antibody via, for example, a peptide linker as provided for herein. In some -36- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT embodiments, the Fc region is an IgG Fc as provided for herein. In some embodiments, the IgG is selected from IgG1, IgG2, IgG3, or IgG4. In some embodiments, the IgG fc is IgG1 Fc as provided for herein. In some embodiments, the antibody comprises an Fc constant region of SEQ ID NO: 26. In some embodiments, the IgG fc is IgG2 Fc as provided for herein. In some embodiments, the antibody comprises an Fc constant region of SEQ ID NO: 27. In some embodiments, the IgG fc is IgG4 Fc as provided for herein. In some embodiments, the antibody comprises an Fc constant region of SEQ ID NO: 28.
[0128] In some embodiments, the targeting moiety binds to CD8 and comprises an HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, LCDR3, VH, and VL as recited in Table 3 and Table 4 below: Table 3 - CD8 targeting moiety CD8AB1 CDR sequences Numberin HCDR1 HCDR2 HCDR3 LCDR1 LCDR2 LCDR3 P QSEQ ID NO: AB ID NO: Region Sequence 60 CD8AB1 VHEVQLQQSGPELVKPGASVKISCKASRYTFTDYNLHWVKLSHEKSLEWIGFIYPYNGGTGYNQKFKNKAKLTVDYSSSTAYMELRSLTSVDAAVYYC P Nlimited to an scFv format where the VH and VL regions are linked with a peptide linker. Examples of peptide linkers that can be used to link various peptides provided for herein include, but are not limited to: (GGGGS)n (SEQ ID NO: 64), wherein each n is independently 1-4. In some embodiments, n is 1. In some embodiments, n is 2. In some embodiments, n is 3. In some embodiments, n is 4. In some embodiments, the variable regions are not linked -37- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT with a peptide linker. In some embodiments, the polypeptide comprises SEQ ID NO: 60 and SEQ ID NO: 61.
[0130] In some embodiments, the targeting moiety comprises a linked peptide represented by a formula of VL-Z-VH, wherein Z is a peptide linker. In some embodiments, the targeting moiety comprises a heavy chain variable region as set forth in SEQ ID NO: 60 linked via a linker sequence GGGGSGGGGSGGGGSGGGGS (SEQ ID NO: 72) to a light chain variable region as set forth in SEQ ID NO: 61. In some embodiments, a targeting moiety comprising a VL linked via a peptide linker to a VH has the sequence as set forth below: NIVLTQSPASLAVSLGQRATISCRASESVDGFGNSFMNWYQQKPGQSPKLLIYLASN LESGVPARFSGSGSRTDFTLTIDPVEADDAATYYCQQNNEDPYTFGGGTKLEIKRGG GGSGGGGSGGGGSGGGGSEVQLQQSGPELVKPGASVKISCKASRYTFTDYNLHWVKL SHEKSLEWIGFIYPYNGGTGYNQKFKNKAKLTVDYSSSTAYMELRSLTSVDAAVYYC ARDHRYNEGVSFDYWGQGTTLTVSS (SEQ ID NO: 62)
[0131] In some embodiments, the targeting moiety comprises a linked peptide represented by a formula of VH-Z-VL, wherein Z is a peptide linker. In some embodiments, the targeting moiety comprises a heavy chain variable region as set forth in SEQ ID NO: 60 linked via a linker sequence GGGGSGGGGSGGGGSGGGGS (SEQ ID NO: 72) to a light chain variable region as set forth in SEQ ID NO: 61. In some embodiments, a targeting moiety comprising a VHlinked via a peptide linker to a VLhas the sequence as set forth below: EVQLQQSGPELVKPGASVKISCKASRYTFTDYNLHWVKLSHEKSLEWIGFIYPYNGG TGYNQKFKNKAKLTVDYSSSTAYMELRSLTSVDAAVYYCARDHRYNEGVSFDYWGQG TTLTVSSGGGGSGGGGSGGGGSGGGGSNIVLTQSPASLAVSLGQRATISCRASESVD GFGNSFMNWYQQKPGQSPKLLIYLASNLESGVPARFSGSGSRTDFTLTIDPVEADDA ATYYCQQNNEDPYTFGGGTKLEIKR (SEQ ID NO: 63)
[0132] In some embodiments, the targeting moiety comprises an amino acid sequence having at least 70% identity to SEQ ID NO: 44, or is substantially similar to SEQ ID NO: 44, or is an active fragment of SEQ ID NO: 44. In some embodiments, the targeting moiety comprises an amino acid sequence having least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to SEQ ID NO: 44. In some embodiments, the targeting moiety comprises an amino acid sequence of SEQ ID NO: 44.
[0133] In some embodiments, the targeting moiety comprises an amino acid sequence having at least 70% identity to SEQ ID NO: 45, or is substantially similar to SEQ ID NO: 45, or is an active fragment of SEQ ID NO: 45. In some embodiments, the targeting -38- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT moiety comprises an amino acid sequence having least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to SEQ ID NO: 45. In some embodiments, the targeting moiety comprises an amino acid sequence of SEQ ID NO: 45.
[0134] In some embodiments, the targeting moiety comprises an amino acid sequence having at least 70% identity to SEQ ID NO: 62, or is substantially similar to SEQ ID NO: 62, or is an active fragment of SEQ ID NO: 62. In some embodiments, the targeting moiety comprises an amino acid sequence having least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to SEQ ID NO: 62. In some embodiments, the targeting moiety comprises an amino acid sequence of SEQ ID NO: 62.
[0135] In some embodiments, the targeting moiety comprises an amino acid sequence having at least 70% identity to SEQ ID NO: 63, or is substantially similar to SEQ ID NO: 63, or is an active fragment of SEQ ID NO: 63. In some embodiments, the targeting moiety comprises an amino acid sequence having least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to SEQ ID NO: 63. In some embodiments, the targeting moiety comprises an amino acid sequence of SEQ ID NO: 63.
[0136] In some embodiments, the targeting moiety as provided for herein is attached to the surface of the virus through a stalk portion, S1. In some embodiments, the targeting moiety is represented by the formula T-S1, wherein T is a targeting moiety as provided for herein and S1 is the stalk portion. In some embodiments, the stalk portion, S1, is as provided in PCT Publication No. WO2024026284, which is hereby incorporated by reference in its entirety. In some embodiments, the stalk portion, S1, comprises a variant Fc protein as provided for herein and is given by the formula L1-Fc-L2-X1, wherein L1 is a linker or absent; Fc is the variant Fc protein; L2 is a linker or absent; and X1 is a polypeptide comprising a transmembrane domain. Thus, in some embodiments, the formula representing the targeting moiety may also be written T-L1-Fc-L2-X1. In some embodiments, the stalk portion, S1, does not comprise a variant Fc region and is given by the formula L3-X1, wherein L3 is a flexible polypeptide linker and X1 is a polypeptide comprising a transmembrane domain. Thus, in some embodiments, the formula representing the targeting moiety may also be written T-L3-X1. In some -39- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT embodiments, the polypeptide comprising a transmembrane domain, X1, comprises a polypeptide having a formula of ECD-TM-ICD, wherein ECD is an extracellular domain, or a fragment thereof, of a cell surface protein, or is absent, TM is a transmembrane domain of a transmembrane protein, and ICD is an intracellular domain of a protein or is a protein that facilitates the incorporation of the targeting moiety into the envelope of the viral particle, or is absent. Accordingly, the formulas representing the targeting moieties linked to the stalk portions may also be written as T-L1-Fc-L2-ECD-TM-ICD or T-L3-ECD-TM-ICD. Exemplary identities for L1, L2, L3, Fc, ECD, TM, and ICD may be found in PCT Publication No. WO2024026284, which is hereby incorporated by reference in its entirety.
[0137] In some embodiments, the targeting moiety comprises a formula of T- L1-Fc-L2-ECD-TM-ICD. In some embodiments, T comprises an amino acid sequence having at least 90% identity to SEQ ID NO: 44, SEQ ID NO: 45, SEQ ID NO: 62, or SEQ ID NO: 63. In some embodiments, L1 is present and comprises the amino acid sequence of SEQ ID NO: 72. In some embodiments, Fc comprises an amino acid sequence having at least 90% identity to SEQ ID NO: 82. In some embodiments, L2 is absent. In some embodiments, ECD comprises an amino acid sequence having at least 90% identity to SEQ ID NO: 83: KIEVMYPPPYLDNEKSNGTIIHVKGKHLCPSPLFPGPSKP (SEQ ID NO: 83) In some embodiments, TM comprises an amino acid sequence having at least 90% identity to SEQ ID NO: 84: FWVLVVVGGVLACYSLLVTVAFIIFWV (SEQ ID NO: 84) In some embodiments, ICD comprises an amino acid sequence comprising an env incorporation motif, wherein the env incorporation motif comprises an amino acid sequence of SEQ ID NO: 85: NRVRQGYS (SEQ ID NO: 85)
[0138] In some embodiments, the targeting moiety comprises a formula of T- L1-Fc-L2-ECD-TM-ICD. In some embodiments, T comprises an amino acid sequence of SEQ ID NO: 44, SEQ ID NO: 45, SEQ ID NO: 62, or SEQ ID NO: 63. In some embodiments, L1 is present and comprises the amino acid sequence of SEQ ID NO: 72. In some embodiments, Fc comprises an amino acid sequence of SEQ ID NO: 82. In some embodiments, L2 is absent. In some embodiments, ECD comprises an amino acid sequence of SEQ ID NO: 83. In some embodiments, TM comprises an amino acid sequence of SEQ ID NO: 84. In some embodiments, ICD comprises an amino acid sequence comprising an env incorporation motif, wherein the env incorporation motif comprises an amino acid sequence of SEQ ID NO: 85. -40- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT
[0139] In some embodiments, the targeting moiety comprises a formula of T- L1-Fc-L2-ECD-TM-ICD. In some embodiments, T comprises an amino acid sequence of SEQ ID NO: 44 or SEQ ID NO: 45. In some embodiments, L1 is present and comprises the amino acid sequence of SEQ ID NO: 72. In some embodiments, Fc comprises an amino acid sequence of SEQ ID NO: 82. In some embodiments, L2 is absent. In some embodiments, ECD comprises an amino acid sequence of SEQ ID NO: 83. In some embodiments, TM comprises an amino acid sequence of SEQ ID NO: 84. In some embodiments, ICD comprises an amino acid sequence comprising an env incorporation motif, wherein the env incorporation motif comprises an amino acid sequence of SEQ ID NO: 85.
[0140] In some embodiments, the targeting moiety comprises a formula of T- L1-Fc-L2-ECD-TM-ICD. In some embodiments, T comprises an amino acid sequence of SEQ ID NO: 45. In some embodiments, L1 is present and comprises the amino acid sequence of SEQ ID NO: 72. In some embodiments, Fc comprises an amino acid sequence of SEQ ID NO: 82. In some embodiments, L2 is absent. In some embodiments, ECD comprises an amino acid sequence of SEQ ID NO: 83. In some embodiments, TM comprises an amino acid sequence of SEQ ID NO: 84. In some embodiments, ICD comprises an amino acid sequence comprising an env incorporation motif, wherein the env incorporation motif comprises an amino acid sequence of SEQ ID NO: 85.
[0141] In some embodiments, the targeting moiety comprises a formula of T- L3-ECD-TM-ICD. In some embodiments, T comprises an amino acid sequence having at least 90% identity to SEQ ID NO: 44, SEQ ID NO: 45, SEQ ID NO: 62, or SEQ ID NO: 63. In some embodiments, L3 comprises an amino acid sequence of SEQ ID NO: 64, wherein n is 1, 2, or 4. In some embodiments, ECD comprises an amino acid sequence having at least 90% identity to SEQ ID NO: 86: FVPVFLPAKPTTTPAPRPPTPAPTIASQPLSLRPEACRPAAGGAVHTRGLDFACD (SEQ ID NO: 86) In some embodiments, TM comprises an amino acid sequence having at least 90% identity to SEQ ID NO: 87: IYIWAPLAGTCGVLLLSLVITLYCNHRN (SEQ ID NO: 87) In some embodiments, ICD comprises an amino acid sequence comprising an env incorporation motif, wherein the env incorporation motif comprises an amino acid sequence of SEQ ID NO: 85 or SEQ ID NO: 88: GGTETSQVAPA (SEQ ID NO: 88). -41- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT
[0142] In some embodiments, the targeting moiety comprises a formula of T- L3-ECD-TM-ICD. In some embodiments, T comprises an amino acid sequence of SEQ ID NO: 44, SEQ ID NO: 45, SEQ ID NO: 62, or SEQ ID NO: 63. In some embodiments, L3 comprises an amino acid sequence of SEQ ID NO: 64, wherein n is 1, 2, or 4. In some embodiments, ECD comprises an amino acid sequence of SEQ ID NO: 86. In some embodiments, TM comprises an amino acid sequence of SEQ ID NO: 87. In some embodiments, ICD comprises an amino acid sequence comprising an env incorporation motif, wherein the env incorporation motif comprises an amino acid sequence of SEQ ID NO: 85 or SEQ ID NO: 88.
[0143] In some embodiments, the targeting moiety comprises a formula of T- L3-ECD-TM-ICD. In some embodiments, T comprises an amino acid sequence of SEQ ID NO: 44 or SEQ ID NO: 45. In some embodiments, L3 comprises an amino acid sequence of SEQ ID NO: 64, wherein n is 1, 2, or 4. In some embodiments, ECD comprises an amino acid sequence of SEQ ID NO: 86. In some embodiments, TM comprises an amino acid sequence of SEQ ID NO: 87. In some embodiments, ICD comprises an amino acid sequence comprising an env incorporation motif, wherein the env incorporation motif comprises an amino acid sequence of SEQ ID NO: 85 or SEQ ID NO: 88.
[0144] In some embodiments, the targeting moiety comprises a formula of T- L3-ECD-TM-ICD. In some embodiments, T comprises an amino acid sequence of SEQ ID NO: 45. In some embodiments, L3 comprises an amino acid sequence of SEQ ID NO: 64, wherein n is 1, 2, or 4. In some embodiments, ECD comprises an amino acid sequence of SEQ ID NO: 86. In some embodiments, TM comprises an amino acid sequence of SEQ ID NO: 87. In some embodiments, ICD comprises an amino acid sequence comprising an env incorporation motif, wherein the env incorporation motif comprises an amino acid sequence of SEQ ID NO: 85 or SEQ ID NO: 88.
[0145] In some embodiments, the targeting moiety comprising a formula of T- S1 comprises 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 NO: 89: METDTLLLWVLLLWVPGSTGDSAQVQLQQPGAELVKPGASVKLSCKASGYPFTSYWIHWVKQ RPGRGLEWLGRIDPNSGDTKYNEKFKNKATLTVDKSSTTAYMQLSSLTSEDSAVYYCARSPYYS NDNSMDYWGQGTSVTVSSGGGGSGGGGSGGGGSGGGGSDILLTQSPAILSVSPGERVSFSCR ASQSIGTSIHWYQQRTNDSPRLLIKYASESISGIPSRFSGSGSGTDFTLSINSVESEDIADYYCQQS NSWPTTFGGGTKLEIKRASGGGGSGGGGSGGGGSEPKSCDKTHTCPPCPAPEAAGGPSVFLFP PKPKDTLMASRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYASTYRVVSVLT VLAQDWLNGKEYKCKVSNKALGAPIEKTISKAKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGF YPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHN AYTQKSLSLSPGKKIEVMYPPPYLDNEKSNGTIIHVKGKHLCPSPLFPGPSKPFWVLVVVGGVLA CYSLLVTVAFIIFWVRSKRSRLLHSDYMNRVRQGYS (SEQ ID NO: 89) -42- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT In some embodiments, the targeting moiety comprising a formula of T-S1 comprises an amino acid sequence having 90% identity to SEQ ID NO: 89. In some embodiments, the targeting moiety comprising a formula of T-S1 comprises an amino acid sequence having 95% identity to SEQ ID NO: 89. In some embodiments, the targeting moiety comprising a formula of T-S1 comprises an amino acid sequence having 98% identity to SEQ ID NO: 89. In some embodiments, the targeting moiety comprising a formula of T-S1 comprises an amino acid sequence of SEQ ID NO: 89.
[0146] In some embodiments, the viral particle comprising a mutant VSV-G protein as provided for herein and comprising a targeting moiety as provided for herein further comprises a nucleic acid molecule encoding for a heterologous molecule of interest or “cargo.” For example, heterologous molecule of interest is meant to refer to any product that may be encoded by a nucleic acid molecule. As non-limiting examples, “cargo” or “heterologous molecule of interest” may refer to an siRNA, an shRNA, a peptide, a polypeptide, a protein, a viral payload, a viral genome, or a combination thereof. In some embodiments, the polypeptide is a chimeric antigen receptor (“CAR”).
[0147] A “chimeric antigen receptor” or “CAR” as used herein refers to an antigen-binding domain that is fused, directly, or indirectly (e.g. via a hinge or transmembrane domain to an intracellular signaling domain capable of activating or stimulating an immune cell. Most commonly, the CAR's extracellular binding domain is composed of a single chain variable fragment (scFv) derived from fusing the variable heavy and light regions of a murine or humanized monoclonal antibody. Alternatively, scFvs may be used that are derived from Fab's (instead of from an antibody, e.g., obtained from Fab libraries). In various embodiments, this scFv is fused to a transmembrane domain and then to an intracellular signaling domain. However, the antigen binding domain can be any molecule that can bind to the to target on the cell. For example, the antigen binding domain of a CAR can be an antibody, a scFv antibody, an antigen binding domain, an ankyrin repeat (e.g. DARPIN), a VHH domain antibody, a nanobody, single domain antibody, a FN3 domain, or any combination thereof. In some embodiments, a CAR includes those that solely provide CD3ζ signals upon antigen binding. In some embodiments, the CAR includes those that provide both costimulation (e.g. CD28 or CD137) and activation (CD3 ζ). In some embodiments, the CARs include those that provide multiple costimulation (e.g. CD28 and CD137) and activation (CD3ζ). In various embodiments, the CAR is selected to have high affinity or avidity for the antigen. In some embodiments, the CAR comprises the 4-1BB domain as well. These are merely illustrative in -43- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT nature and are not limiting to the present embodiments and any chimeric antigen receptor can be delivered in conjunction with the viral particles and vectors provided for herein. These are non-limiting examples of CARs and any CAR construct could be encoded for by the nucleic acid molecule.
[0148] In some embodiments, the antigen-binding domain of the CAR comprises a VH domain, a VL domain, or a VH and a VL domain. In some embodiments, the VH domain comprises an amino acid sequence having at least 75%, 80%, 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO: 73, or any value or range in-between. EVQLVESGGGLVQPGRSLRLSCAASGFTFNDYAMHWVRQAPGKGLEWVSTISWNSGS IGYADSVKGRFTISRDNAKKSLYLQMNSLRAEDTALYYCAKDIQYGNYYYGMDVWGQ GTTVTVSS(SEQ ID NO: 73) In some embodiments, the VHdomain comprises an amino acid sequence having at least 90% identity to SEQ ID NO: 73. In some embodiments, the VH domain comprises an amino acid sequence having at least 95% identity to SEQ ID NO: 73. In some embodiments, the VH domain comprises an amino acid sequence having at least 98% identity to SEQ ID NO: 73. In some embodiments, the VH domain comprises an amino acid sequence having at least 99% identity to SEQ ID NO: 73. In some embodiments, the VH domain comprises an amino acid sequence having the sequence of SEQ ID NO: 73.
[0149] In some embodiments, the VL domain comprises an amino acid sequence having at least 75%, 80%, 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO: 74, or any value or range in- between. EIVLTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATG IPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQRSNWPITFGQGTRLEIK (SEQ ID NO: 74) In some embodiments, the VL domain comprises an amino acid sequence having at least 90% identity to SEQ ID NO: 74. In some embodiments, the VL domain comprises an amino acid sequence having at least 95% identity to SEQ ID NO: 74. In some embodiments, the VL domain comprises an amino acid sequence having at least 98% identity to SEQ ID NO: 74. In some embodiments, the VL domain comprises an amino acid sequence having at least 99% -44- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT identity to SEQ ID NO: 74. In some embodiments, the VL domain comprises an amino acid sequence having the sequence of SEQ ID NO: 74.
[0150] In some embodiments, the antigen-binding domain of the CAR comprises a VH domain and a VL domain. In some embodiments, the VH and VL domain are not linked by a linker peptide. In some embodiments, the VH and VL domain are linked by a linker peptide, such as those as provided for herein, including but not limited to: (GGGGS)n (SEQ ID NO: 64), wherein each n is independently 1-5. In some embodiment n is 1. In some embodiment n is 2. In some embodiment n is 3. In some embodiment n is 4. In some embodiment n is 5.
[0151] In some embodiments, the antigen-binding domain of the CAR comprising a VH domain and a VL domain comprises a VH domain having at least 75%, 80%, 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO: 73, and comprises a VL having at least 75%, 80%, 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO: 74. In some embodiments, the antigen-binding domain of the CAR comprising a VH domain and a VL domain comprises a VH domain having at least 75%, 80%, 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO: 73, and comprises a VL having at least 90% identity to SEQ ID NO: 74. In some embodiments, the antigen-binding domain of the CAR comprising a VH domain and a VL domain comprises a VH domain having at least 75%, 80%, 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO: 73, and comprises a VL having at least 95% identity to SEQ ID NO: 74. In some embodiments, the antigen-binding domain of the CAR comprising a VH domain and a VL domain comprises a VH domain having at least 75%, 80%, 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO: 73, and comprises a VL having at least 98% identity to SEQ ID NO: 74. In some embodiments, the antigen-binding domain of the CAR comprising a VH domain and a VL domain comprises a VH domain having at least 75%, 80%, 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO: 73, and comprises a VL having at least 99% identity to SEQ ID NO: 74. In some embodiments, the antigen-binding domain of the CAR comprising a VH domain and a VL domain comprises a VH domain having at least 75%, 80%, 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO: 73, and comprises a VL having the sequence of SEQ ID NO: 74. In some embodiments, the antigen-binding domain of the CAR comprising a VH domain and a VL -45- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT domain comprises a VH domain having at least 90% identity to SEQ ID NO: 73, and comprises a VL having at least 75%, 80%, 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO: 74. In some embodiments, the antigen- binding domain of the CAR comprising a VH domain and a VL domain comprises a VH domain having at least 95% identity to SEQ ID NO: 73, and comprises a VL having at least 75%, 80%, 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO: 74. In some embodiments, the antigen-binding domain of the CAR comprising a VH domain and a VL domain comprises a VH domain having at least 98% identity to SEQ ID NO: 73, and comprises a VL having at least 75%, 80%, 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO: 74. In some embodiments, the antigen-binding domain of the CAR comprising a VH domain and a VL domain comprises a VH domain having at least 99% identity to SEQ ID NO: 73, and comprises a VL having at least 75%, 80%, 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO: 74. In some embodiments, the antigen-binding domain of the CAR comprising a VH domain and a VL domain comprises a VH domain having an amino acid sequence of SEQ ID NO: 73, and comprises a VL having at least 75%, 80%, 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO: 74. In some embodiments, the antigen-binding domain of the CAR comprising a VH domain and a VL domain comprises a VH domain having at least 90% identity to SEQ ID NO: 73, and comprises a VL having at least 90% identity to SEQ ID NO: 74. In some embodiments, the antigen-binding domain of the CAR comprising a VH domain and a VL domain comprises a VH domain having at least 95% identity to SEQ ID NO: 73, and comprises a VL having at least 90% identity to SEQ ID NO: 74. In some embodiments, the antigen-binding domain of the CAR comprising a VH domain and a VL domain comprises a VH domain having at least 90% identity to SEQ ID NO: 73, and comprises a VL having at least 95% identity to SEQ ID NO: 74. In some embodiments, the antigen- binding domain of the CAR comprising a VH domain and a VL domain comprises a VH domain having at least 95% identity to SEQ ID NO: 73, and comprises a VL having at least 95% identity to SEQ ID NO: 74. In some embodiments, the antigen-binding domain of the CAR comprising a VH domain and a VL domain comprises a VH domain having at least 98% identity to SEQ ID NO: 73, and comprises a VL having at least 98% identity to SEQ ID NO: 74. In some embodiments, the antigen-binding domain of the CAR comprising a VH domain and a VL domain comprises a VH domain having at least 99% identity to SEQ ID NO: 73, and comprises a VL having at least 99% identity to SEQ ID NO: 74. In some embodiments, the antigen- -46- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT binding domain of the CAR comprising a VH domain and a VL domain comprises a VH domain having an amino acid sequence of SEQ ID NO: 73, and comprises a VL having an amino acid sequence of SEQ ID NO: 74.
[0152] In some embodiments, the antigen-binding domain of the CAR comprises a formula of VH-Z-VL, wherein VH is a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 73, Z is a linker comprising the amino acid sequence GGGGSGGGGSGGGGS (SEQ ID NO: 77), and VL is a light chain variable region comprising the amino acid sequence of SEQ ID NO: 74. In some embodiments, the antigen-binding domain of the CAR comprising a formula of VH-Z-VL has an amino acid sequence as set forth below: EVQLVESGGGLVQPGRSLRLSCAASGFTFNDYAMHWVRQAPGKGLEWVSTISWNSGS IGYADSVKGRFTISRDNAKKSLYLQMNSLRAEDTALYYCAKDIQYGNYYYGMDVWGQ GTTVTVSSGGGGSGGGGSGGGGSEIVLTQSPATLSLSPGERATLSCRASQSVSSYLA WYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQR SNWPITFGQGTRLEIK (SEQ ID NO: 75) In some embodiments, the antigen-binding domain of the CAR comprises 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 a sequence of SEQ ID NO: 75. In some embodiments, the antigen-binding domain of the CAR comprises an amino acid sequence having at least 90% identity to a sequence of SEQ ID NO: 75. In some embodiments, the antigen-binding domain of the CAR comprises an amino acid sequence having at least 95% identity to a sequence of SEQ ID NO: 75. In some embodiments, the antigen-binding domain of the CAR comprises an amino acid sequence having at least 98% identity to a sequence of SEQ ID NO: 75. In some embodiments, the antigen-binding domain of the CAR comprises an amino acid sequence having at least 99% identity to a sequence of SEQ ID NO: 75. In some embodiments, the antigen-binding domain of the CAR comprises the amino acid sequence of SEQ ID NO: 75.
[0153] In some embodiments, the antigen-binding domain of the CAR comprises a formula of VL-Z-VH, wherein VL is a light chain variable region comprising the amino acid sequence of SEQ ID NO: 74, Z is a linker comprising the amino acid sequence GGGGSGGGGSGGGGS (SEQ ID NO: 77), and VH is a light chain variable region comprising the amino acid sequence of SEQ ID NO: 73. In some embodiments, the antigen-binding domain of the CAR comprising a formula of VL-Z-VH has an amino acid sequence as set forth below: -47- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT EIVLTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATG IPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQRSNWPITFGQGTRLEIKGGGGSGG GGSGGGGSEVQLVESGGGLVQPGRSLRLSCAASGFTFNDYAMHWVRQAPGKGLEWVS TISWNSGSIGYADSVKGRFTISRDNAKKSLYLQMNSLRAEDTALYYCAKDIQYGNYY YGMDVWGQGTTVTVSS (SEQ ID NO: 76) In some embodiments, the antigen-binding domain of the CAR comprises 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 a sequence of SEQ ID NO: 76. In some embodiments, the antigen-binding domain of the CAR comprises an amino acid sequence having at least 90% identity to a sequence of SEQ ID NO: 76. In some embodiments, the antigen-binding domain of the CAR comprises an amino acid sequence having at least 95% identity to a sequence of SEQ ID NO: 76. In some embodiments, the antigen-binding domain of the CAR comprises an amino acid sequence having at least 98% identity to a sequence of SEQ ID NO: 76. In some embodiments, the antigen-binding domain of the CAR comprises an amino acid sequence having at least 99% identity to a sequence of SEQ ID NO: 76. In some embodiments, the antigen-binding domain of the CAR comprises the amino acid sequence of SEQ ID NO: 76.
[0154] In some embodiments, the antigen-binding domain of the CAR comprises a VH domain, a VL domain, or a VH and a VL domain. In some embodiments, the VH domain comprises an amino acid sequence having at least 75%, 80%, 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO: 78, or any value or range in-between. DIVLTQSPAILSASPGEKVTMTCRASSSVNYMDWYQKKPGSSPKPWIYATSNLASGV PARFSGSGSGTSYSLTISRVEAEDAATYYCQQWSFNPPTFGGGTKLEIKGSTS (SEQ ID NO: 78) In some embodiments, the VH domain comprises an amino acid sequence having at least 90% identity to SEQ ID NO: 78. In some embodiments, the VH domain comprises an amino acid sequence having at least 95% identity to SEQ ID NO: 78. In some embodiments, the VH domain comprises an amino acid sequence having at least 98% identity to SEQ ID NO: 78. In some embodiments, the VH domain comprises an amino acid sequence having at least 99% identity to SEQ ID NO: 78. In some embodiments, the VH domain comprises an amino acid sequence having the sequence of SEQ ID NO: 78. -48- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT
[0155] In some embodiments, the VL domain comprises an amino acid sequence having at least 75%, 80%, 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO: 79, or any value or range in- between. EVQLQQSGAELVKPGASVKMSCKASGYTFTSYNMHWVKQTPGQGLEWIGAIYPGNGD TSYNQKFKGKATLTADKSSSTAYMQLSSLTSEDSADYYCARSNYYGSSYWFFDVWGA GTTVTVSS (SEQ ID NO: 79) In some embodiments, the VL domain comprises an amino acid sequence having at least 90% identity to SEQ ID NO: 79. In some embodiments, the VL domain comprises an amino acid sequence having at least 95% identity to SEQ ID NO: 79. In some embodiments, the VL domain comprises an amino acid sequence having at least 98% identity to SEQ ID NO: 79. In some embodiments, the VL domain comprises an amino acid sequence having at least 99% identity to SEQ ID NO: 79. In some embodiments, the VLdomain comprises an amino acid sequence having the sequence of SEQ ID NO: 79.
[0156] In some embodiments, the antigen-binding domain of the CAR comprising a VH domain and a VL domain comprises a VH domain having at least 75%, 80%, 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO: 78, and comprises a VL having at least 75%, 80%, 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO: 79. In some embodiments, the antigen-binding domain of the CAR comprising a VH domain and a VL domain comprises a VH domain having at least 75%, 80%, 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO: 78, and comprises a VL having at least 90% identity to SEQ ID NO: 79. In some embodiments, the antigen-binding domain of the CAR comprising a VH domain and a VL domain comprises a VH domain having at least 75%, 80%, 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO: 78, and comprises a VL having at least 95% identity to SEQ ID NO: 79. In some embodiments, the antigen-binding domain of the CAR comprising a VH domain and a VL domain comprises a VH domain having at least 75%, 80%, 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO: 78, and comprises a VL having at least 98% identity to SEQ ID NO: 79. In some embodiments, the antigen-binding domain of the CAR comprising a VHdomain and a VLdomain comprises a VHdomain having at least 75%, 80%, 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, -49- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT 99%, or 100% identity to SEQ ID NO: 78, and comprises a VL having at least 99% identity to SEQ ID NO: 79. In some embodiments, the antigen-binding domain of the CAR comprising a VH domain and a VL domain comprises a VH domain having at least 75%, 80%, 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO: 78, and comprises a VL having the sequence of SEQ ID NO: 79. In some embodiments, the antigen-binding domain of the CAR comprising a VH domain and a VL domain comprises a VH domain having at least 90% identity to SEQ ID NO: 78, and comprises a VL having at least 75%, 80%, 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO: 79. In some embodiments, the antigen- binding domain of the CAR comprising a VH domain and a VL domain comprises a VH domain having at least 95% identity to SEQ ID NO: 78, and comprises a VL having at least 75%, 80%, 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO: 79. In some embodiments, the antigen-binding domain of the CAR comprising a VH domain and a VL domain comprises a VH domain having at least 98% identity to SEQ ID NO: 78, and comprises a VL having at least 75%, 80%, 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO: 79. In some embodiments, the antigen-binding domain of the CAR comprising a VH domain and a VL domain comprises a VH domain having at least 99% identity to SEQ ID NO: 78, and comprises a VL having at least 75%, 80%, 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO: 79. In some embodiments, the antigen-binding domain of the CAR comprising a VH domain and a VL domain comprises a VH domain having an amino acid sequence of SEQ ID NO: 78, and comprises a VL having at least 75%, 80%, 85%, 85%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO: 79. In some embodiments, the antigen-binding domain of the CAR comprising a VH domain and a VL domain comprises a VH domain having at least 90% identity to SEQ ID NO: 78, and comprises a VL having at least 90% identity to SEQ ID NO: 79. In some embodiments, the antigen-binding domain of the CAR comprising a VH domain and a VL domain comprises a VH domain having at least 95% identity to SEQ ID NO: 78, and comprises a VL having at least 90% identity to SEQ ID NO: 79. In some embodiments, the antigen-binding domain of the CAR comprising a VH domain and a VL domain comprises a VH domain having at least 90% identity to SEQ ID NO: 78, and comprises a VL having at least 95% identity to SEQ ID NO: 79. In some embodiments, the antigen- binding domain of the CAR comprising a VH domain and a VL domain comprises a VH domain having at least 95% identity to SEQ ID NO: 78, and comprises a VL having at least 95% identity -50- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT to SEQ ID NO: 79. In some embodiments, the antigen-binding domain of the CAR comprising a VH domain and a VL domain comprises a VH domain having at least 98% identity to SEQ ID NO: 78, and comprises a VL having at least 98% identity to SEQ ID NO: 79. In some embodiments, the antigen-binding domain of the CAR comprising a VH domain and a VL domain comprises a VH domain having at least 99% identity to SEQ ID NO: 78, and comprises a VL having at least 99% identity to SEQ ID NO: 79. In some embodiments, the antigen- binding domain of the CAR comprising a VH domain and a VL domain comprises a VH domain having an amino acid sequence of SEQ ID NO: 78, and comprises a VL having an amino acid sequence of SEQ ID NO: 79.
[0157] In some embodiments, the antigen-binding domain of the CAR comprises a formula of VH-Z-VL, wherein VH is a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 78, Z is a linker comprising the amino acid sequence GGGGSGGGGSGGGGS (SEQ ID NO: 77), and VL is a light chain variable region comprising the amino acid sequence of SEQ ID NO: 79. In some embodiments, the antigen-binding domain of the CAR comprising a formula of VH-Z-VL has an amino acid sequence as set forth below: DIVLTQSPAILSASPGEKVTMTCRASSSVNYMDWYQKKPGSSPKPWIYATSNLASGV PARFSGSGSGTSYSLTISRVEAEDAATYYCQQWSFNPPTFGGGTKLEIKGSTSGGGG SGGGGSGGGGSSEVQLQQSGAELVKPGASVKMSCKASGYTFTSYNMHWVKQTPGQGL EWIGAIYPGNGDTSYNQKFKGKATLTADKSSSTAYMQLSSLTSEDSADYYCARSNYY GSSYWFFDVWGAGTTVTVSS (SEQ ID NO: 80) In some embodiments, the antigen-binding domain of the CAR comprises 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 a sequence of SEQ ID NO: 80. In some embodiments, the antigen-binding domain of the CAR comprises an amino acid sequence having at least 90% identity to a sequence of SEQ ID NO: 80. In some embodiments, the antigen-binding domain of the CAR comprises an amino acid sequence having at least 95% identity to a sequence of SEQ ID NO: 80. In some embodiments, the antigen-binding domain of the CAR comprises an amino acid sequence having at least 98% identity to a sequence of SEQ ID NO: 80. In some embodiments, the antigen-binding domain of the CAR comprises an amino acid sequence having at least 99% identity to a sequence of SEQ ID NO: 80. In some embodiments, the antigen-binding domain of the CAR comprises the amino acid sequence of SEQ ID NO: 80. -51- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT
[0158] In some embodiments, the antigen-binding domain of the CAR comprises a formula of VL-Z-VH, wherein VL is a light chain variable region comprising the amino acid sequence of SEQ ID NO: 79, Z is a linker comprising the amino acid sequence GGGGSGGGGSGGGGS (SEQ ID NO: 77), and VH is a light chain variable region comprising the amino acid sequence of SEQ ID NO: 78. In some embodiments, the antigen-binding domain of the CAR comprising a formula of VL-Z-VH has an amino acid sequence as set forth below: SEVQLQQSGAELVKPGASVKMSCKASGYTFTSYNMHWVKQTPGQGLEWIGAIYPGNG DTSYNQKFKGKATLTADKSSSTAYMQLSSLTSEDSADYYCARSNYYGSSYWFFDVWG AGTTVTVSSGGGGSGGGGSGGGGSDIVLTQSPAILSASPGEKVTMTCRASSSVNYMD WYQKKPGSSPKPWIYATSNLASGVPARFSGSGSGTSYSLTISRVEAEDAATYYCQQW SFNPPTFGGGTKLEIKGSTS (SEQ ID NO: 81) In some embodiments, the antigen-binding domain of the CAR comprises 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 a sequence of SEQ ID NO: 81. In some embodiments, the antigen-binding domain of the CAR comprises an amino acid sequence having at least 90% identity to a sequence of SEQ ID NO: 81. In some embodiments, the antigen-binding domain of the CAR comprises an amino acid sequence having at least 95% identity to a sequence of SEQ ID NO: 81. In some embodiments, the antigen-binding domain of the CAR comprises an amino acid sequence having at least 98% identity to a sequence of SEQ ID NO: 81. In some embodiments, the antigen-binding domain of the CAR comprises an amino acid sequence having at least 99% identity to a sequence of SEQ ID NO: 81. In some embodiments, the antigen-binding domain of the CAR comprises the amino acid sequence of SEQ ID NO: 81.
[0159] In some embodiments, the antigen-binding domain of the CAR comprises rituximab, ocrelizumab, obinutuzumab, ofatumumab, ibritumomab tiuxetan, tositumomab, or ublituximab. In some embodiment, the antigen-binding domain comprises rituximab. In some embodiment, the antigen-binding domain comprises ofatumumab. In some embodiments, the CAR comprises the 4-1BB domain as well. These are merely illustrative in nature and are not limiting to the present embodiments and any chimeric antigen receptor can be delivered in conjunction with the viral particles and vectors provided for herein. These are non-limiting examples of CARs and any CAR construct could be encoded for by the nucleic acid molecule. -52- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT
[0160] In some embodiments, the CAR comprises an amino acid sequence that is at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a sequence of SEQ ID NO: 90: MALPVTALLLPLALLLHAARPGSEVQLVESGGGLVQPGRSLRLSCAASGFTF NDYAMHWVRQAPGKGLEWVSTISWNSGSIGYADSVKGRFTISRDNAKKSLYL QMNSLRAEDTALYYCAKDIQYGNYYYGMDVWGQGTTVTVSSGGGGSGGGGSG GGGSEIVLTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLI YDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQRSNWPITFGQ GTRLEIKSGLDFVPVFLPAKPTTTPAPRPPTPAPTIASQPLSLRPEACRPAA GGAVHTRGLDFACDIYIWAPLAGTCGVLLLSLVITLYCNHRNKRGRKKLLYI FKQPFMRPVQTTQEEDGCSCRFPEEEEGGCELRVKFSRSADAPAYQQGQNQL YNELNLGRREEYDVLDKRRGRDPEMGGKPRRKNPQEGLYNELQKDKMAEAYS EIGMKGERRRGKGHDGLYQGLSTATKDTYDALHMQALPPR (SEQ ID NO: 90) or is substantially similar to SEQ ID NO: 90, or is an active fragment of SEQ ID NO: 90. In some embodiments, the CAR comprises an amino acid sequence that is at least 90% identical to a sequence of SEQ ID NO: 90. In some embodiments, the CAR comprises an amino acid sequence that is at least 95% identical to a sequence of SEQ ID NO: 90. In some embodiments, the CAR comprises an amino acid sequence that is at least 98% identical to a sequence of SEQ ID NO: 90. In some embodiments, the CAR comprises an amino acid sequence of SEQ ID NO: 90. In some embodiments, the sub domains of the CAR (e.g., the antigen binding domain, hinge domain, transmembrane domain, costimulatory domain, signaling domain) are as provided in PCT Publication No. WO2024026284, which is hereby incorporated by reference in its entirety.
[0161] The preceding embodiments describing CARs within the scope of the present application are exemplary only and are not meant to be limiting in any way. Various CAR constructs are known in the art and any such CAR molecule is within the scope of the instant application. Additional or alternative CARs that are within the scope of the present application may be found at least in WO2023 / 114884, WO2023 / 154858, WO2024 / 026284, WO2024 / 258866, and WO2024 / 259279, U.S. Patent Nos. 11,767,366B2, 12,104,177B2, and 12,252,512B2, and U.S. Patent Publication Nos. 2024 / 0287472 and 2023 / 0293688, each of which is hereby incorporated by reference in their entirety.
[0162] In some embodiments, the pseudotyped viral particle further comprises a heterologous nucleic acid molecule encoding a cargo of interest. The nucleic acid molecule may be useful for modulating the expression of a target gene. In some embodiments, the cargo can be used to modulate the activity of a cell or express a protein that is trafficked to the surface of the target cell. Therefore, in some embodiments, the nucleic acid may comprise an siRNA -53- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT or an shRNA. The nucleic acid may also encode for a cargo of interest. Therefore, in some embodiments, the cargo of interest may comprise a polypeptide or portion thereof, a protein or portion thereof, a chimeric antigen receptor or portion thereof, or a tumor antigen or a portion thereof. In some embodiments, the cargo of interest is an antibody that is produced by the virus, which can then be secreted by the cell that is infected with the virus. The term “protein” can refer to any polypeptide that carries a native function in a cellular environment. Therefore, in some embodiments, the protein encoded by the nucleic acid cargo of interest may comprise an enzyme, a nuclear receptor, a transporter, a ribosomal protein, a membrane bound protein, a cytoplasmic protein, a G-protein coupled receptor, a voltage gated ion channel, a secretory protein, a mitochondria protein, a cytokine, a chimeric antigen receptor, a tumor antigen, or a portion or chimeric species thereof.
[0163] Without being bound to any particular theory, the viral particle comprising the mutant VSV-G protein as provided for herein that comprises a targeting moiety can be used to express the heterologous molecule of interest in the target cell. Thus, for example, the CAR can be expressed in a T cell that is targeted by a viral particle pseudotyped with a VSV-G protein as provided for herein. Where the T cell is the intended target the viral particle can comprise a targeting moiety that binds to a target on the surface of a T cell, such as, but not limited to CD2, CD3, CD4, CD5, CD7 or CD8. In some embodiments, the target is CD2. In some embodiments, the target is CD3. In some embodiments, the target is CD4. In some embodiments, the target is CD5. In some embodiments, the target is CD6. In some embodiments, the target is CD7. In some embodiments, the target is CD8.
[0164] In some embodiments, the pseudotyped viral particle is a recombinant lentivirus. In some embodiments, the recombinant pseudotyped viral particle is replication competent. In some embodiments, the recombinant pseudotyped viral particle is replication incompetent. Exemplary viral particles:
[0165] In some embodiments, a viral particle is provided, the the viral particle comprising a heterologous viral glycoprotein and a targeting moiety, wherein the heterologous viral glycoprotein comprises an amino acid sequence selected from SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 24, or SEQ ID NO: 25 and wherein the targeting moiety comprises an amino acid sequence of SEQ ID NO: 89. In some embodiments, the viral particle further comprises a nucleic acid molecule encoding a heterologous molecule of interest. In some embodiments, the heterologous molecule of interest is as provided for herein. In some -54- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT embodiments, the heterologous molecule of interest is a CAR as provided for herein. In some embodiments, the CAR comprises an amino acid sequence having at least 85% identity to SEQ ID NO: 90, at least 90% identity to SEQ ID NO: 90, at least 95% identity to SEQ ID NO: 90. at least 99% identity to SEQ ID NO: 90, or at least 100% identity to SEQ ID NO: 90.
[0166] In some embodiments, a viral particle is provided, the the viral particle comprising a heterologous viral glycoprotein and a targeting moiety, wherein the heterologous viral glycoprotein comprises an amino acid sequence selected from SEQ ID NO: 22 or SEQ ID NO: 23, and wherein the targeting moiety comprises an amino acid sequence of SEQ ID NO: 89. In some embodiments, the viral particle further comprises a nucleic acid molecule encoding a heterologous molecule of interest. In some embodiments, the heterologous molecule of interest is as provided for herein. In some embodiments, the heterologous molecule of interest is a CAR as provided for herein. In some embodiments, the CAR comprises an amino acid sequence having at least 85% identity to SEQ ID NO: 90, at least 90% identity to SEQ ID NO: 90, at least 95% identity to SEQ ID NO: 90. at least 99% identity to SEQ ID NO: 90, or at least 100% identity to SEQ ID NO: 90.
[0167] In some embodiments, a viral particle is provided, the the viral particle comprising a heterologous viral glycoprotein and a targeting moiety, wherein the heterologous viral glycoprotein comprises an amino acid sequence of SEQ ID NO: 22 and wherein the targeting moiety comprises an amino acid sequence of SEQ ID NO: 89. In some embodiments, the viral particle further comprises a nucleic acid molecule encoding a heterologous molecule of interest. In some embodiments, the heterologous molecule of interest is as provided for herein. In some embodiments, the heterologous molecule of interest is a CAR as provided for herein. In some embodiments, the CAR comprises an amino acid sequence having at least 85% identity to SEQ ID NO: 90, at least 90% identity to SEQ ID NO: 90, at least 95% identity to SEQ ID NO: 90. at least 99% identity to SEQ ID NO: 90, or at least 100% identity to SEQ ID NO: 90.
[0168] In some embodiments, a viral particle is provided, the the viral particle comprising a heterologous viral glycoprotein and a targeting moiety, wherein the heterologous viral glycoprotein comprises an amino acid sequence of SEQ ID NO: 23 and wherein the targeting moiety comprises an amino acid sequence of SEQ ID NO: 89. In some embodiments, the viral particle further comprises a nucleic acid molecule encoding a heterologous molecule of interest. In some embodiments, the heterologous molecule of interest is as provided for herein. In some embodiments, the heterologous molecule of interest is a CAR as provided for herein. In some embodiments, the CAR comprises an amino acid sequence having at least 85% -55- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT identity to SEQ ID NO: 90, at least 90% identity to SEQ ID NO: 90, at least 95% identity to SEQ ID NO: 90. at least 99% identity to SEQ ID NO: 90, or at least 100% identity to SEQ ID NO: 90. Enumerated Embodiments: 1. A method of determining the infectious titer of a pharmaceutical composition, including, but not limited to a sterile-filtered pharmaceutical composition, comprising a viral vector comprising a nucleic acid molecule encoding for a chimeric antigen receptor, the method comprising: contacting ex vivo an immune cell preparation comprising immune cells infected with the pharmaceutical composition with a first antibody and a second antibody, wherein the first antibody binds to an immune cell surface marker (ICSM) of interest and the second antibody is an idiotypic antibody that binds to the antigen binding domain of the chimeric antigen receptor to produced an antibody labeled immune cell preparation; analyzing the antibody labeled immune cell preparation to determine the number of cells that are positive for the immune cell surface marker of interest (ICSM+) and positive for the antigen binding domain of the chimeric antigen receptor (CAR+) to determine the infectious titer of the pharmaceutical composition comprising the virus. 2. The method of embodiment 1, wherein the transducing units / mL (“TU”). 3. The method of embodiment 1, wherein the infectious titer is calculated by the following formula: IU=[(%CAR+ / ICSM+) x (Total number of cells seeded in well) x (Dilution Factor)] / (Total Volume of inocolum and cell volume(mL)). 4. The method of any one of embodiments 1-3, wherein the first antibody is labeled with a first label and the second antibody is labeled with a second label, wherein the first label and the second label are different. 5. The method of any one of embodiments 1-4, wherein the analyzing is performed by flow cytometry to detect the cells that are ICSM+ and CAR+. 6. The method of any one of embodiments 1-5, wherein the analyzing comprises fixing the cells prior to performing flow cytometry. 7. The method of embodiment 6, wherein fixing cells comprises fixing the cells with formaldehyde. 8. The method of embodiment 7, wherein the fixing comprises fixing the cells in PBS and formaldehyde. -56- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT 9. The method of embodiments 7 or 8, wherein the fixing comprises fixing the cells in 3.7% formaldehyde in PBS (e.g., 10% Formalin). 10. The method of any one of embodiments 1-9, further comprising infecting a population of cells with the pharmaceutical composition comprising the virus encoding for the chimeric antigen receptor to produce the immune cell preparation infected with the pharmaceutical composition. 11. The method of embodiment 11, wherein the viral vector is a lentivirus. 12. The method of embodiment 11, wherein the lentivirus is a pseudotyped lentivirus. 13. The method of embodiment 12, wherein the pseudotyped lentivirus is pseudotyped with VSV-G. 14. The method of any one of embodiments 1-13, wherein the immune cells infected with the pharmaceutical composition are T cells. 15. The method of embodiment 14, wherein the T cells are CD7+ cells. 16. The method of any one of embodiments 1-15, wherein the first antibody specifically binds to CD7 17. The method of any one of embodiments 1-16, wherein the antigen binding domain binds to CD19 or CD20. 18. The method of embodiment 17, wherein the second antibody specifically binds to the antigen binding domain residues that bind to CD20. 19. The method of embodiment 17, wherein the second antibody specifically binds to the antigen binding domain residues that bind to CD19. 20. A method of treating a disease in a subject with a pharmaceutical composition comprising a virus comprising a nucleic acid molecule encoding for a chimeric antigen receptor, the method comprising: determining the infectious titer according to any one of embodiments 1-19; and administering an effective amount of the pharmaceutical composition to the subject the pharmaceutical composition in an amount based on the determined infectious titer. 21. The method of claim 20, wherein the pharmaceutical composition is administered parenterally. 22. The method of any one of claims 1-21, wherein the viral vector comprises a VSV-G polypeptide. 23. The method of any one of the preceding embodiments, wherein the viral vector, such as a lentiviral vector, is pseudotyped with a VSV-G polypeptide comprising a mutation that corresponds to a mutation at position 182 of SEQ ID NO: 2. -57- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT 24. The method of embodiments 22 or 23, wherein the VSV-G polypeptide comprises an amino acid sequence of SEQ ID NO: 2 with a mutation at position 182 and has at least 95% identity to SEQ ID NO: 2. 25. The method of embodiments 22-25, wherein the VSV-G polypeptide comprises a I182E or I182D mutation as compared to SEQ ID NO: 2. 26. The method of any one of embodiments 22-25, wherein the VSV-G polypeptide comprises an amino acid sequence of SEQ ID NO: 1 with a mutation at position 198 and has at least 70% identity to SEQ ID NO: 2. 27. The method of any one of embodiments 22-26, wherein the VSV-G polypeptide comprises a mutation that corresponds to I182D or I182E as compared to a sequence of SEQ ID NO: 2. 28. The method of any one of embodiments 22-27, wherein the VSV-G polypeptide comprises an amino acid sequence at least 95% identical to a sequence of SEQ ID NO: 4. 29. The method of any one of embodiments 22-28, wherein the VSV-G polypeptide comprises an amino acid sequence of SEQ ID NO: 4. 30. The method of any one of embodiments 22-27, wherein the VSV-G polypeptide comprises an amino acid sequence at least 95% identical to a sequence of SEQ ID NO: 5. 31. The method of any one of embodiments 22-30, wherein the VSV-G polypeptide comprises an amino acid sequence of SEQ ID NO: 5. 32. The method of any one of embodiments 22-31, wherein the VSV-G polypeptide further comprises a mutation in the VSV-G protein that corresponds to a position of 8, 10, 47, 209 and / or 354 as compared to SEQ ID NO: 2. 33. The method of any one of embodiments 22-32, wherein the VSV-G polypeptide further comprises a mutation that corresponds to position 8 in SEQ ID NO: 2, wherein the mutation is any amino acid different from the amino acid indicated at that position in SEQ ID NO: 2, except Y. 34. The method of any one of embodiments 22-33, wherein the VSV-G polypeptide further comprises a mutation that corresponds to position 209 in SEQ ID NO: 2, wherein the mutation is any amino acid different from the amino acid indicated at that position in SEQ ID NO: 2, except H. -58- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT 35. The method of any one of embodiments 22-34, wherein the VSV-G polypeptide further comprises a mutation that corresponds to position 47 in SEQ ID NO: 2, wherein the mutation is any amino acid different from the amino acid indicated at that position in SEQ ID NO: 2, except K or R. 36. The method of any one of embodiments 22-35, wherein the VSV-G polypeptide further comprises a mutation that corresponds to position 354 in SEQ ID NO: 2, wherein the mutation is any amino acid different from the amino acid indicated at that position in SEQ ID NO: 2, except K or R. 37. The method of any one of embodiments 22-36, wherein the VSV-G polypeptide further comprises a mutation that corresponds to position 10 in SEQ ID NO: 2, wherein the mutation is any amino acid different from the amino acid indicated at that position in SEQ ID NO: 2, except Q or N. 38. The method of any one of embodiments 22-37, wherein the VSV-G polypeptide further comprises a substitution at position 47 or at position 354, or at both positions 47 and 354, wherein each position is, independently, substituted by A, G, F, Q, or N. 39. The method of any one of embodiments 22-38, wherein the VSV-G polypeptide comprises a substitution at position 8, wherein the substitution is H8A, H8I, H8V, H8L, and the like. 40. The method of any one of embodiments 22-39, wherein the VSV-G polypeptide comprises a substitution at position 47, wherein the substitution is K47Q or K47N. 41. The method of any one of embodiments 22-40, wherein the VSV-G polypeptide comprises a substitution H8A and / or K47Q mutation. 42. The method of any one of embodiments 22-41, wherein the VSV-G polypeptide comprises a Q10A, Q10R, or Q10K substitution. 43. The method of any one of embodiments 22-42, wherein the VSV-G polypeptide further comprises a mutation that corresponds to a mutation at positions 214 and / or 352 of SEQ ID -59- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT NO: 2. 44. The method of embodiment 43, wherein the VSV-G polypeptide comprises a T214N and / or T352A mutation. 45. The method of claim any one of embodiments 22-44, wherein the viral particle comprises a VSV-G polypeptide comprising a substitution at positions I182 and at least one of T214, and T352 of SEQ ID NO: 2. 46. The method of embodiment 45, wherein the VSV-G polypeptide comprises substitutions at positions I182, T214, and T352 of SEQ ID NO: 2. 47. The method of embodiments 87 or 88, wherein the substitution at position 182 is I182D or I182E, the substitution at position 214 is T214N, and the substitution at position 352 is T352A. 48. The method of any one of embodiments 45-47, wherein the VSV-G polypeptide comprises a sequence of SEQ ID NO: 23, SEQ ID NO: 22, SEQ ID NO: 24 or SEQ ID NO: 25. 49. The method of any one of embodiments 45-47, wherein the VSV-G polypeptide comprises a sequence of SEQ ID NO: 23. 50. The method of any one of embodiments 45-47, wherein the VSV-G polypeptide comprises a sequence of SEQ ID NO: 22. 51. The method of any one of embodiments 45-47, wherein the VSV-G polypeptide comprises a sequence of SEQ ID NO: 24. 52. The method of any one of embodiments 45-47, wherein the VSV-G polypeptide comprises a sequence of SEQ ID NO: 25. 53. The method of any one of embodiments 1-52, wherein the viral vector comprises a targeting moiety. -60- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT 54. The method of embodiment 53 wherein the targeting moiety binds to CD7. 55. The method of embodiment 54, wherein the targeting moiety comprises a polypeptide comprising: (i) a heavy chain variable region comprising heavy chain CDRl, CDR2, and CDR3 sequences, wherein the heavy chain CDR1 sequence has the amino acid sequence of SEQ ID NO: 30; the heavy chain CDR2 has the amino acid sequence of SEQ ID NO: 31; and the heavy chain CDR3 sequence has the amino acid sequence of SEQ ID NO: 32, or variants of any of the foregoing; and (ii) a light chain variable region comprising light chain CDR1, CDR2, and CDR3 sequences, wherein the light chain CDR1 sequence has the amino acid sequence of SEQ ID NO: 33; the light chain CDR2 sequence has the amino acid sequence of SEQ ID NO: 34; and the light chain CDR3 sequence has the amino acid sequence of SEQ ID NO: 35; or variants of any of the foregoing. 56. The method of embodiments 54 or 55, wherein the targeting moiety comprises a heavy chain variable region (VH) comprising an amino acid sequence of SEQ ID NO: 42 and a light chain variable region (VL) comprising an amino acid sequence of SEQ ID NO: 43. 57. The method of any one of embodiments 54-56, wherein the targeting moiety comprises an antigen binding domain comprising an amino acid sequence of SEQ ID NO: 44 or SEQ ID NO: 45. 58. The method of embodiment 53, wherein the targeting moiety binds to CD8. 59. The method of embodiment 58, wherein the targeting moiety comprises a polypeptide comprising: (i) a heavy chain variable region comprising heavy chain CDRl, CDR2, and CDR3 sequences, wherein the heavy chain CDR1 sequence has the amino acid sequence of SEQ ID NO: 48; the heavy chain CDR2 has the amino acid sequence of SEQ ID NO: 49; and the heavy chain CDR3 sequence has the amino acid sequence of SEQ ID NO: 50, or variants of any of the foregoing; and (ii) a light chain variable region comprising light chain CDR1, CDR2, and CDR3 sequences, wherein the light chain CDR1 sequence has the amino acid sequence of SEQ ID NO: 51; the light chain CDR2 sequence has the amino acid sequence of SEQ ID NO: 52; and the light chain CDR3 sequence has the amino acid sequence of SEQ ID NO: 53; or variants of any of the foregoing. -61- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT 60. The method of embodiments 58 or 59, wherein the targeting moiety comprises a heavy chain variable region (VH) comprising an amino acid sequence of SEQ ID NO: 60 and a light chain variable region (VL) comprising an amino acid sequence of SEQ ID NO: 61. 61. The method of any one of embodiments 58-60, wherein the targeting moiety comprises an antigen binding domain comprising an amino acid sequence of SEQ ID NO: 62 or SEQ ID NO: 63. 62. The method of any one of embodiments 53-61, wherein the targeting moiety comprises a formula of T-S1, wherein T is a target binding domain and S1 is a stalk portion, wherein the targeting moiety is attached to the surface of the viral vector through a stalk portion, S1,. 63. The method of embodiment 62, wherein the stalk portion, S1 comprises a variant Fc protein. 64. The method of embodiment 63, wherein the stalk portion, S1, comprises a formula of L1-Fc-L2-X1, wherein: L1 is a linker or absent; Fc is a variant Fc protein; L2 is a linker or absent; and X1 is a polypeptide comprising the transmembrane domain, wherein the targeting moiety having the formula T-S1 has a formula of T-L1-Fc-L2-X1. 65. The method of embodiment 64, wherein X1 comprises a polypeptide having a formula of ECD-TM-ICD, wherein: ECD is an extracellular domain, or a fragment thereof, of a cell surface protein, or absent; TM is a transmembrane domain of a transmembrane protein; and ICD is an intracellular domain or a protein that facilitates incorporation of the targeting moiety into the envelope of the viral particle, or absent, wherein the targeting moiety having the formula of T-L1-Fc-L2-X1 has a formula of T-L1-Fc- L2-ECD-TM-ICD. -62- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT 66. The method of embodiments 64 or 65, wherein: T comprises an amino acid sequence of SEQ ID NO: 44, SEQ ID NO: 45, SEQ ID NO: 62, or SEQ ID NO: 63; L1 comprises the amino acid sequence of SEQ ID NO: 72; Fc comprises the amino acid sequence of SEQ ID NO: 82; L2 is absent; ECD comprises the amino acid sequence of SEQ ID NO: 83; TM comprises the amino acid sequence of SEQ ID NO: 84; and ICD comprises an amino acid sequence comprising an env incorporation motif, wherein the env incorporation motif comprises an amino acid sequence of SEQ ID NO: 85. 67. The method of embodiment 64, wherein the stalk portion, S1 does not comprise a variant Fc protein. 68. The method of embodiment 67, wherein the stalk portion S1 comprises a formula of L3- X1, wherein: L3 is a flexible peptide linker, and X1 is a polypeptide comprising a transmembrane domain, wherein the targeting moiety having the formula T-S1 has a formula of T-L3-X1. 69. The method of embodiment 68, wherein X1 comprises a polypeptide having a formula of ECD-TM-ICD, wherein: ECD is an extracellular domain, or a fragment thereof, of a cell surface protein, or absent; TM is a transmembrane domain of a transmembrane protein; and ICD is an intracellular domain or a protein that facilitates incorporation of the targeting moiety into the envelope of the viral particle, or absent, wherein the targeting moiety having the formula of T-L3-X1 has a formula of T-L3-ECD-TM- ICD. 70. The method of embodiment 69, wherein: T comprises an amino acid sequence of SEQ ID NO: 44, SEQ ID NO: 45, SEQ ID NO: 62, or SEQ ID NO: 63; L3 comprises the amino acid sequence of SEQ ID NO: 64, wherein n is 1, 2, or 4; -63- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT ECD comprises the amino acid sequence of SEQ ID NO: 86; TM comprises the amino acid sequence of SEQ ID NO: 87; and ICD comprises an amino acid sequence comprising an env incorporation motif, wherein the env incorporation motif comprises an amino acid sequence of SEQ ID NO: 85 or SEQ ID NO: 88. 71. The method of embodiment 62, wherein the targeting moiety comprising a formula of T-S1 comprises an amino acid sequence having at least 90% identity to SEQ ID NO: 89. 72. The method of embodiment 62, wherein the targeting moiety comprising a formula of T-S1 comprises an amino acid sequence having at least 95% identity to SEQ ID NO: 89. 73. The method of embodiment 62, wherein the targeting moiety comprising a formula of T-S1 comprises an amino acid sequence of SEQ ID NO: 89. 74. The method of any one of embodiments 1-73, wherein the CAR comprises an antigen binding domain comprising an antibody, or a fragment thereof. 75. The method of embodiment 74, wherein the antibody, or fragment thereof is an antibody, a scFv antibody, an antigen binding domain, an ankyrin repeat, a VHH domain antibody, a nanobody, a single domain antibody, or an FN3 antibody. 76. The method of any one of embodiments 1-75, wherein the antigen binding domain of the CAR binds to CD20. 77. The method of embodiment 76, wherein the antigen binding domain that binds to CD20 comprises a polypeptide comprising a light chain and a heavy chain comprising: a heavy chain variable region of the heavy chain having at least 90% identity to an amino acid sequence of SEQ ID NO: 73; and a light chain variable region of the light chain having at least 90% identity to an amino acid sequence of SEQ ID NO: 74. 78. The method of embodiments 76 or 77, wherein the antigen binding domain that binds to CD20 comprises an amino acid sequence of SEQ ID NO: 75 or SEQ ID NO: 76. -64- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT 79. The method of any one of embodiments 76-78, wherein the antigen binding domain that binds to CD20 comprises a polypeptide comprising a light chain and a heavy chain comprising: a heavy chain variable region of the heavy chain having at least 90% identity to an amino acid sequence of SEQ ID NO: 78; and a light chain variable region of the light chain having at least 90% identity to an amino acid sequence of SEQ ID NO: 79. 80. The method of embodiment 78 or 79, wherein the antigen binding domain that binds to CD20 comprises an amino acid sequence of SEQ ID NO: 80 or SEQ ID NO: 81. 81. The method of any one of embodiments 74-80, wherein the CAR comprises an amino acid sequence having at least 90% identity to SEQ ID NO: 90. 82. The method of any one of embodiments 74-80, wherein the CAR comprises an amino acid sequence having at least 95% identity to SEQ ID NO: 90. 83. The method of any one of embodiments 74-80, wherein the CAR comprises an amino acid sequence of SEQ ID NO: 90. Examples
[0169] Various embodiments are further described in detail by reference to the following examples. These examples are provided for purposes of illustration only, and are not intended to be limiting unless otherwise specified. Thus, embodiments should in no way be construed as being limited to the following examples, but rather, should be construed to encompass any and all variations which become evident as a result of the teaching provided herein.
[0170] Example 1: Viral Vector Manufacturing Process. The pharmaceutical copmosition comprising the viral vector was prepared according to the methods provided for in PCT / US2024 / 014002, which is hereby incorporated by reference in its entirety. This method of preparation is just one example and is non-limiting as any method of making a pharmaceutical composition comprising a viral vector can be utilized.
[0171] Example 2: Infectious Titer Assay
[0172] Immune cells, such as SupT1 cells were contacted (incubated) with various dilutions of a pharmaceutical composition comprising a viral vector comprising a nucleic acid molecule encoding a CAR, wherein the CAR comprises an antigen domain that binds to CD20, -65- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT such as those provided for herein. The virus also comprised a targeting domain that binds to CD7 to facilitate targeting of CD7 positive T cells. The virus was also pseudotyped with VSV- G 182E as provided for herein. The cells were allowed to incubate with the virus for 24 hours to allow for viral transduction. After 24 hours the media was removed and replaced. The media was changed periodically until day 7 post innoculation (Day 0 is considered when the cells are infected with the virus). The cells were isolated and analyzed in well formats or processed for flow cytometry. The cells can optionally be fixed in formaldehyde, such as 3.7% formaldehyde in PBS (e.g.10% Formalin). The cells were labeled with an antibody that binds to CD7 and an idiotypic antibody that binds to the scFv of the CAR that binds to CD20.
[0173] The cells were analyzed by flow cytometry. Based on the various dilutions, 2- 20% CAR+ cells (i.e., cells that are CD7+ and CAR+) were used to calculate titer as they are assumed to result from a single transduction event as per Poisson distribution and were sufficiently above the background of flow cytometry staining. The infectious titer was determined by the following formula: ^^ =^% "#$$% &'(^^) ^# "#$$% *$+,#-^ ) ,2,+$ -1$0,12 / ! ,.+ / %-0",12 / 32$0 # ^ !^
[0174] This assay can also be automated at any step to remove potential operator error. For example, the media exchange during the culturing step can be performed by automation.
[0175] The infectious titer was found to be sufficient.
[0176] Example 3:
[0177] Lentiviral vector (LVV) potency, as measured by transduction efficiency, is a Critical Quality Attribute (CQA) that must be monitored for every LVV sample. At Interius, the in vitro potency of LVV samples is assessed in an infectious titer assay via the transduction of SupT1, a suspension T cell line, that serve as model CD7+ target cells. Transduction of target cells by the LVV, encoding a CAR20 protein, is detected through antibody staining of SupT1 cells using an anti-idiotype monoclonal antibody targeted to the scFv domain of the CAR20 protein using flow cytometry. LVV containing samples are serially diluted and added to a fixed amount of target cells in a 96 well plate format. The transduced cells are incubated for 7 days, with intermittent medium refresh, followed by live cell staining for CD7+ and CAR+. The transducing units (TU) per mL are calculated by assessing the CAR+ cells amongst total live SupT1 cells assuming a Poisson distribution of single cell infections in the range of 2 – 20%. -66- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT
[0178] The manual execution of the ITA method is a labor-intensive, multi-day process consisting of many discrete steps, followed by a long day of live cell staining and signal acquisition by flow cytometry. Standard 96 well plate reading flow cytometers are not well suited for high-throughput flow cytometry. To support the sample numbers required to develop multiple process development efforts simultaneously, a high throughput solution was required.
[0179] To this end, we have developed a fully automated, multi-step method covering sample dilution, SupT1 transduction, medium refresh, moving from 96-well to 384- well plates, 384-well live cell staining and HT flow cytometry on a Sartorius iQue, followed by automated data reduction. Each of these discrete steps is designed to reduce hands-on time and eliminate operator to operator variability while providing the added benefits of increased throughput and speed. Importantly, the same assay framework can be utilized for different products and target cells with minor modifications.
[0180] The ITA Assay is a resource intensive 7D assay requiring accurate delivery of cells and samples, multiple media changes, cell staining, and flow cytometry analysis of transgene(+) T-cells as illustrated in FIG.1.
[0181] Analysis by flow cytometry to determine the percentage of cells that were transduced. 2-20% CAR+ cells are used to calculate titer as they are assumed to result from a single transduction event as per Poisson distribution AND are sufficiently above the background of flow cytometry staining. Linearity criteria are applied to serial dilutions in series, and the corresponding ITA values calculated as follows: ^^ =^% "#$$% &'(^^) ^# "#$$% *$+,#-^ ) ,2,+$ -1$0,12 / ! ,.+ / %-0",12 / 32$0 # ^ !^
[0182] Various steps were automated. As each automation step was demonstrated to be comparable to manual operations, it was incorporated into routine running of the ITA assay. The assay was currently fully automated providing the capability to keep pace with the ever- expanding upstream and downstream process development needs, while increasing the accuracy and decreasing operator hands-on time, allowing for historically comparable data throughout the process while improving the assay. Additionally, automation of operations enables multiple operators to contribute without introducing variability.
[0183] For example, sample dilutions for the ITA assay require precision pipetting for both non-concentrated samples (transfer of larger volumes) and concentrated samples (transfer of small volumes for large dilutions). Artel MVS technology was used to ensure accuracy of pipetting of the Tecan Freedom EVO for sample dilutions. Plating and dilution of samples by the EVO frees assay operators to prepare cells and overcomes the potential for human error in -67- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT sample preparation - and standardizes pipetting. Utilizing Excel with VBA to generate worklists, the Tecan EVO dilutes samples neat to 8000-fold, independently, on 1 - 96 samples in a 40-minute run (maximum – depending on number of samples, degree of dilution). The Tecan precisely and accurately moves samples from stock tubes to assay-ready plates at desired dilutions. Cell plating during LVV transduction was also automated. Settling during cell addition for transduction may increase assay variation, when compared to manual plating. For example, SUP-T1 cell health decline is of primary concern potentially resulting from exposure to ambient conditions (air and temperature). To evaluate this, SUP-T1 cells were plated manually across a 96 well plate and compared to a CyBio Felix plating the following conditions: 0.5, 1.0, 2.0, 2.5, 3.03.5 and 4 hours. The times chosen bracket operational times of the assay from minimal runs (e.g., 2 plates) to extensive plating conditions for maximal plates at 4 hours. Cell Titer Glo was used to measure ATP as an indirect measure of cell number and viability. Plates were read after a 10-minute recommended incubation and then all together at the end of the assay. There was no indication of decreased viability over 4H of ambient exposure. Analysis demonstrated no patterns to small variation in cells numbers. This data is illustrated in FIG.2.
[0184] To pursue the assay comparability to historical data, we wanted to ensure that automated media exchange was similar to the manual method, with respect to cell loss and assay performance. The manual media exchange process uses visualization to avoid aspiration of the pellet. There are several challenges in this process, including a variation in pellet size, and pellet location in the well due to relative position in the plate during centrifugation. Initial automated evaluation demonstrated an aspiration height of 0.5mm above the well bottom removed almost all the liquid, and all the cells were recovered as assessed by vi-cell counts of select wells across various plate positions. FIG.3A-3B illustrates the results of evaluating the Cybio Felix’s ability to avoid aspirating the pellet and the level of media aspiration that was most similar to manual manipulations by assessing the percentage of transduced cells at the end of 7 days (FIGS 3A-3C), and calculating corresponding ITA values (FIG. 3D). The data demonstrates that high and low media refresh conditions have little impact on ITA results.
[0185] Finally, it was determined that automated staining was non statistically different and performed similar to the manual method. At day 7, live samples from 4 assays were stained using the Tecan Fluent and analyzed on the Satorius iQue and compared to the same samples stained manually and analyzed on the Beckman CytoFLEX. Briefly, manual staining versus automated staining were compared by evaluating a Deming linear regression to show that the -68- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT process provides data comparable between the two methods. The same antibodies against CD7 and the CD20 scFv were utilized. The same gating strategy was used for both methods.
[0186] The ITA reader comparison illustrated in FIG.4 demonstrated that the assay can be automated without significant loss of signal or sensitivity, nor bias across the ranges of potency tested. The ITA values were comparable between both methods. Thus, the automated staining can be used to decrease operator hands-on time. For example, iQue analysis decreased analysis time from 4H for 4 plates to 1H for 4 plates. This significant time savings reduces costs and increases accuracy over different lots and avoids operator errors.
[0187] Example 4: Treatment of Patients with CD20 Positive Cancer
[0188] A patient presented with a cancer that is CD20 positive. A pharmaceutical composition comprising a viral vector is prepared according to Example 1. The infectious titer of the pharmaceutical composition is determined according to Example 2 or Example 3. An effective amount of the pharmaceutical composition is administered to the patient to treat the cancer.
[0189] Thus, the examples provided for herein demonstrate a flow cytometry assay can be utilized to determine the infectious titer of a viral vector comprising a nucleic acid molecule encoding for a chimeric antigen receptor. This is less time consuming and more straight forward as compared to other methods, including PCR based methods. The accuracy of this method was surprising. These methods can be used to administer a higher dose of a pharmaceutical composition comprising a viral vector in a smaller volume because the determination of the infectious titer is more accurate, which is advantageous to patients being treated with viral vector based therapies.
[0190] This specification contains numerous citations to patents, patent applications, and publications. Each is hereby incorporated by reference for all purposes.
[0191] The specification also makes reference to various sequences, such as those provided herein and below. The alignment of the ectodomains of different VSV-G proteins from different strains is illustrated in FIG 9 of PCT / US2024 / 014002, which is hereby incorporated by reference in its entirety. VSV-G Indiana Full length WT: MKCLLYLAFLFIGVNCKFTIVFPHNQKGNWKNVPSNYHYCPSSSDLNWHNDLIGTALQVKMPKSHKAIQADGWMC HASKWVTTCDFRWYGPKYITHSIRSFTPSVEQCKESIEQTKQGTWLNPGFPPQSCGYATVTDAEAVIVQVTPHHV LVDEYTGEWVDSQFINGKCSNYICPTVHNSTTWHSDYKVKGLCDSNLISMDITFFSEDGELSSLGKEGTGFRSNY FAYETGGKACKMQYCKHWGVRLPSGVWFEMADKDLFAAARFPECPEGSSISAPSQTSVDVSLIQDVERILDYSLC QETWSKIRAGLPISPVDLSYLAPKNPGTGPAFTIINGTLKYFETRYIRVDIAAPILSRMVGMISGTTTERELWDD WAPYEDVEIGPNGVLRTSSGYKFPLYMIGHGMLDSDLHLSSKAQVFEHPHIQDAASQLPDDESLFFGDTGLSKNP IELVEGWFSSWKSSIASFFFIIGLIIGLFLVLRVGIHLCIKLKHTKKRQIYTDIEMNRLGK (SEQ ID NO: -69- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT 1) VSV-G Indiana Ectodomain WT: KFTIVFPHNQKGNWKNVPSNYHYCPSSSDLNWHNDLIGTALQVKMPKSHKAIQADGWMCHASKWVTTCDFRWYGP KYITHSIRSFTPSVEQCKESIEQTKQGTWLNPGFPPQSCGYATVTDAEAVIVQVTPHHVLVDEYTGEWVDSQFIN GKCSNYICPTVHNSTTWHSDYKVKGLCDSNLISMDITFFSEDGELSSLGKEGTGFRSNYFAYETGGKACKMQYCK HWGVRLPSGVWFEMADKDLFAAARFPECPEGSSISAPSQTSVDVSLIQDVERILDYSLCQETWSKIRAGLPISPV DLSYLAPKNPGTGPAFTIINGTLKYFETRYIRVDIAAPILSRMVGMISGTTTERELWDDWAPYEDVEIGPNGVLR TSSGYKFPLYMIGHGMLDSDLHLSSKAQVFEHPHIQDAASQLPDDESLFFGDTGLSKNPIELVEGWFSSWKSSIA SFFFIIGLIIGLFLVLRVGIHLCIKLKHTKKRQIYTDIEMNRLGK (SEQ ID NO: 2) VSV-G Indiana ectodomain I182A: KFTIVFPHNQKGNWKNVPSNYHYCPSSSDLNWHNDLIGTALQVKMPKSHKAIQADGWMCHASKWVTTCDFRWYGP KYITHSIRSFTPSVEQCKESIEQTKQGTWLNPGFPPQSCGYATVTDAEAVIVQVTPHHVLVDEYTGEWVDSQFIN GKCSNYICPTVHNSTTWHSDYKVKGLCDSNLASMDITFFSEDGELSSLGKEGTGFRSNYFAYETGGKACKMQYCK HWGVRLPSGVWFEMADKDLFAAARFPECPEGSSISAPSQTSVDVSLIQDVERILDYSLCQETWSKIRAGLPISPV DLSYLAPKNPGTGPAFTIINGTLKYFETRYIRVDIAAPILSRMVGMISGTTTERELWDDWAPYEDVEIGPNGVLR TSSGYKFPLYMIGHGMLDSDLHLSSKAQVFEHPHIQDAASQLPDDESLFFGDTGLSKNPIELVEGWFSSWKSSIA SFFFIIGLIIGLFLVLRVGIHLCIKLKHTKKRQIYTDIEMNRLGK (SEQ ID NO: 3) VSV-G Indiana ectodomain I182D: KFTIVFPHNQKGNWKNVPSNYHYCPSSSDLNWHNDLIGTALQVKMPKSHKAIQADGWMCHASKWVTTCDFRWYGP KYITHSIRSFTPSVEQCKESIEQTKQGTWLNPGFPPQSCGYATVTDAEAVIVQVTPHHVLVDEYTGEWVDSQFIN GKCSNYICPTVHNSTTWHSDYKVKGLCDSNLDSMDITFFSEDGELSSLGKEGTGFRSNYFAYETGGKACKMQYCK HWGVRLPSGVWFEMADKDLFAAARFPECPEGSSISAPSQTSVDVSLIQDVERILDYSLCQETWSKIRAGLPISPV DLSYLAPKNPGTGPAFTIINGTLKYFETRYIRVDIAAPILSRMVGMISGTTTERELWDDWAPYEDVEIGPNGVLR TSSGYKFPLYMIGHGMLDSDLHLSSKAQVFEHPHIQDAASQLPDDESLFFGDTGLSKNPIELVEGWFSSWKSSIA SFFFIIGLIIGLFLVLRVGIHLCIKLKHTKKRQIYTDIEMNRLGK (SEQ ID NO: 4) VSV-G Indiana ectodomain I182E: KFTIVFPHNQKGNWKNVPSNYHYCPSSSDLNWHNDLIGTALQVKMPKSHKAIQADGWMCHASKWVTTCDFRWYGP KYITHSIRSFTPSVEQCKESIEQTKQGTWLNPGFPPQSCGYATVTDAEAVIVQVTPHHVLVDEYTGEWVDSQFIN GKCSNYICPTVHNSTTWHSDYKVKGLCDSNLESMDITFFSEDGELSSLGKEGTGFRSNYFAYETGGKACKMQYCK HWGVRLPSGVWFEMADKDLFAAARFPECPEGSSISAPSQTSVDVSLIQDVERILDYSLCQETWSKIRAGLPISPV DLSYLAPKNPGTGPAFTIINGTLKYFETRYIRVDIAAPILSRMVGMISGTTTERELWDDWAPYEDVEIGPNGVLR TSSGYKFPLYMIGHGMLDSDLHLSSKAQVFEHPHIQDAASQLPDDESLFFGDTGLSKNPIELVEGWFSSWKSSIA SFFFIIGLIIGLFLVLRVGIHLCIKLKHTKKRQIYTDIEMNRLGK (SEQ ID NO: 5) VSV-G Indiana ectodomain H8A + K47Q: KFTIVFPANQKGNWKNVPSNYHYCPSSSDLNWHNDLIGTALQVKMPQSHKAIQADGWMCHASKWVTTCDFRWYGP KYITHSIRSFTPSVEQCKESIEQTKQGTWLNPGFPPQSCGYATVTDAEAVIVQVTPHHVLVDEYTGEWVDSQFIN GKCSNYICPTVHNSTTWHSDYKVKGLCDSNLISMDITFFSEDGELSSLGKEGTGFRSNYFAYETGGKACKMQYCK HWGVRLPSGVWFEMADKDLFAAARFPECPEGSSISAPSQTSVDVSLIQDVERILDYSLCQETWSKIRAGLPISPV DLSYLAPKNPGTGPAFTIINGTLKYFETRYIRVDIAAPILSRMVGMISGTTTERELWDDWAPYEDVEIGPNGVLR TSSGYKFPLYMIGHGMLDSDLHLSSKAQVFEHPHIQDAASQLPDDESLFFGDTGLSKNPIELVEGWFSSWKSSIA SFFFIIGLIIGLFLVLRVGIHLCIKLKHTKKRQIYTDIEMNRLGK (SEQ ID NO: 6) VSV-G Indiana ectodomain Q10A: KFTIVFPHNAKGNWKNVPSNYHYCPSSSDLNWHNDLIGTALQVKMPKSHKAIQADGWMCHASKWVTTCDFRWYGP KYITHSIRSFTPSVEQCKESIEQTKQGTWLNPGFPPQSCGYATVTDAEAVIVQVTPHHVLVDEYTGEWVDSQFIN GKCSNYICPTVHNSTTWHSDYKVKGLCDSNLISMDITFFSEDGELSSLGKEGTGFRSNYFAYETGGKACKMQYCK HWGVRLPSGVWFEMADKDLFAAARFPECPEGSSISAPSQTSVDVSLIQDVERILDYSLCQETWSKIRAGLPISPV DLSYLAPKNPGTGPAFTIINGTLKYFETRYIRVDIAAPILSRMVGMISGTTTERELWDDWAPYEDVEIGPNGVLR TSSGYKFPLYMIGHGMLDSDLHLSSKAQVFEHPHIQDAASQLPDDESLFFGDTGLSKNPIELVEGWFSSWKSSIA SFFFIIGLIIGLFLVLRVGIHLCIKLKHTKKRQIYTDIEMNRLGK (SEQ ID NO: 7) VSV-G Indiana ectodomain Q10R: KFTIVFPHNRKGNWKNVPSNYHYCPSSSDLNWHNDLIGTALQVKMPKSHKAIQADGWMCHASKWVTTCDFRWYGP KYITHSIRSFTPSVEQCKESIEQTKQGTWLNPGFPPQSCGYATVTDAEAVIVQVTPHHVLVDEYTGEWVDSQFIN GKCSNYICPTVHNSTTWHSDYKVKGLCDSNLISMDITFFSEDGELSSLGKEGTGFRSNYFAYETGGKACKMQYCK -70- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT HWGVRLPSGVWFEMADKDLFAAARFPECPEGSSISAPSQTSVDVSLIQDVERILDYSLCQETWSKIRAGLPISPV DLSYLAPKNPGTGPAFTIINGTLKYFETRYIRVDIAAPILSRMVGMISGTTTERELWDDWAPYEDVEIGPNGVLR TSSGYKFPLYMIGHGMLDSDLHLSSKAQVFEHPHIQDAASQLPDDESLFFGDTGLSKNPIELVEGWFSSWKSSIA SFFFIIGLIIGLFLVLRVGIHLCIKLKHTKKRQIYTDIEMNRLGK (SEQ ID NO: 8) VSV-G Indiana ectodomain Q10K: KFTIVFPHNKKGNWKNVPSNYHYCPSSSDLNWHNDLIGTALQVKMPKSHKAIQADGWMCHASKWVTTCDFRWYGP KYITHSIRSFTPSVEQCKESIEQTKQGTWLNPGFPPQSCGYATVTDAEAVIVQVTPHHVLVDEYTGEWVDSQFIN GKCSNYICPTVHNSTTWHSDYKVKGLCDSNLISMDITFFSEDGELSSLGKEGTGFRSNYFAYETGGKACKMQYCK HWGVRLPSGVWFEMADKDLFAAARFPECPEGSSISAPSQTSVDVSLIQDVERILDYSLCQETWSKIRAGLPISPV DLSYLAPKNPGTGPAFTIINGTLKYFETRYIRVDIAAPILSRMVGMISGTTTERELWDDWAPYEDVEIGPNGVLR TSSGYKFPLYMIGHGMLDSDLHLSSKAQVFEHPHIQDAASQLPDDESLFFGDTGLSKNPIELVEGWFSSWKSSIA SFFFIIGLIIGLFLVLRVGIHLCIKLKHTKKRQIYTDIEMNRLGK (SEQ ID NO: 9) VSV-G New Jersey Full length WT: MLSYLIFALVVSPILGKIEIVFPQHTTGDWKRVPHEYNYCPTSADKNSHGTQTGIPVELTMPKGLTTHQVDGFMC HSALWMTTCDFRWYGPKYITHSIHNEEPTDYQCLEAIKAYKDGVSFNPGFPPQSCGYGTVTDAEAHIVTVTPHSV KVDEYTGEWIDPHFIGGRCKGQICETVHNSTKWFTSSDGESVCSQLFTLVGGTFFSDSEEITSMGLPETGIRSNY FPYVSTEGICKMPFCRKPGYKLKNDLWFQITDPDLDKTVRDLPHIKDCDLSSSIVTPGEHATDISLISDVERILD YALCQNTWSKIEAGEPITPVDLSYLGPKNPGAGPVFTIINGSLHYFMSKYLRVELESPVIPRMEGKVAGTRIVRQ LWDQWFPFGEVEIGPNGVLKTKQGYKFPLHIIGTGEVDNDIKMERIVKHWEHPHIEAAQTFLKKDDTEEVLYYGD TGVSKNPVELVEGWFSGWRSSIMGVLAVIIGFVILIFLIRLIGVLSSLFRQKRRPIYKSDVEMAHFR (SEQ ID NO: 10) VSV-G New Jersey ectodomain WT: KIEIVFPQHTTGDWKRVPHEYNYCPTSADKNSHGTQTGIPVELTMPKGLTTHQVDGFMCHSALWMTTCDFRWYGP KYITHSIHNEEPTDYQCLEAIKAYKDGVSFNPGFPPQSCGYGTVTDAEAHIVTVTPHSVKVDEYTGEWIDPHFIG GRCKGQICETVHNSTKWFTSSDGESVCSQLFTLVGGTFFSDSEEITSMGLPETGIRSNYFPYVSTEGICKMPFCR KPGYKLKNDLWFQITDPDLDKTVRDLPHIKDCDLSSSIVTPGEHATDISLISDVERILDYALCQNTWSKIEAGEP ITPVDLSYLGPKNPGAGPVFTIINGSLHYFMSKYLRVELESPVIPRMEGKVAGTRIVRQLWDQWFPFGEVEIGPN GVLKTKQGYKFPLHIIGTGEVDNDIKMERIVKHWEHPHIEAAQTFLKKDDTEEVLYYGDTGVSKNPVELVEGWFS GWRSSIMGVLAVIIGFVILIFLIRLIGVLSSLFRQKRRPIYKSDVEMAHFR (SEQ ID NO: 11) VSV-G Marraba Full length WT: MLRLFLFCFLALGAHSKFTIVFPHHQKGNWKNVPSTYHYCPSSSDQNWHNDLTGVSLHVKIPKSHKAIQADGWMC HAAKWVTTCDFRWYGPKYITHSIHSMSPTLEQCKTSIEQTKQGVWINPGFPPQSCGYATVTDAEVVVVQATPHHV LVDEYTGEWIDSQLVGGKCSKEVCQTVHNSTVWHADYKITGLCESNLASVDITFFSEDGQKTSLGKPNTGFRSNH FAYESGEKACRMQYCTQWGIRLPSGVWFELVDKDLFQAAKLPECPRGSSISAPSQTSVDVSLIQDVERILDYSLC QETWSKIRAKLPVSPVDLSYLAPKNPGSGPAFTIINGTLKYFETRYIRVDISNPIIPHMVGTMSGTTTERELWND WYPYEDVEIGPNGVLKTPTGFKFPLYMIGHGMLDSDLHKSSQAQVFEHPHAKDAASQLPDDETLFFGDTGLSKNP VELVEGWFSSWKSTLASFFLIIGLGVALIFIIRIIVAIRYKYKGRKTQKIYNDVEMSRLGNK (SEQ ID NO: 12) VSV-G Marraba ectodomain WT: KFTIVFPHHQKGNWKNVPSTYHYCPSSSDQNWHNDLTGVSLHVKIPKSHKAIQADGWMCHAAKWVTTCDFRWYGP KYITHSIHSMSPTLEQCKTSIEQTKQGVWINPGFPPQSCGYATVTDAEVVVVQATPHHVLVDEYTGEWIDSQLVG GKCSKEVCQTVHNSTVWHADYKITGLCESNLASVDITFFSEDGQKTSLGKPNTGFRSNHFAYESGEKACRMQYCT QWGIRLPSGVWFELVDKDLFQAAKLPECPRGSSISAPSQTSVDVSLIQDVERILDYSLCQETWSKIRAKLPVSPV DLSYLAPKNPGSGPAFTIINGTLKYFETRYIRVDISNPIIPHMVGTMSGTTTERELWNDWYPYEDVEIGPNGVLK TPTGFKFPLYMIGHGMLDSDLHKSSQAQVFEHPHAKDAASQLPDDETLFFGDTGLSKNPVELVEGWFSSWKSTLA SFFLIIGLGVALIFIIRIIVAIRYKYKGRKTQKIYNDVEMSRLGNK (SEQ ID NO: 13) VSV-G Carajas Full length WT: MKMKMVIAGLILCIGILPAIGKITISFPQSLKGDWRPVPKGYNYCPTSADKNLHGDLIDIGLRLRAPKSFKGISA DGWMCHAARWITTCDFRWYGPKYITHSIHSFRPSNDQCKEAIRLTNEGNWINPGFPPQSCGYASVTDSESVVVTV -71- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT TKHQVLVDEYSGSWIDSQFPGGSCTSPICDTVHNSTLWHADHTLDSICDQEFVAMDAVLFTESGKFEEFGKPNSG IRSNYFPYESLKDVCQMDFCKRKGFKLPSGVWFEIEDAEKSHKAQVELKIKRCPHGAVISAPNQNAADINLIMDV ERILDYSLCQATWSKIQNKEALTPIDISYLGPKNPGPGPAFTIINGTLHYFNTRYIRVDIAGPVTKEITGFVSGT STSRVLWDQWFPYGENSIGPNGLLKTASGYKYPLFMVGTGVLDADIHKLGEATVIEHPHAKEAQKVVDDSEVIFF GDTGVSKNPVEVVEGWFSGWRSSLMSIFGIILLIVCLVLIVRILIALKYCCVRHKKRTIYKEDLEMGRIPRRA (SEQ ID NO: 14) VSV-G Carajas ectodomain WT: KITISFPQSLKGDWRPVPKGYNYCPTSADKNLHGDLIDIGLRLRAPKSFKGISADGWMCHAARWITTCDFRWYGP KYITHSIHSFRPSNDQCKEAIRLTNEGNWINPGFPPQSCGYASVTDSESVVVTVTKHQVLVDEYSGSWIDSQFPG GSCTSPICDTVHNSTLWHADHTLDSICDQEFVAMDAVLFTESGKFEEFGKPNSGIRSNYFPYESLKDVCQMDFCK RKGFKLPSGVWFEIEDAEKSHKAQVELKIKRCPHGAVISAPNQNAADINLIMDVERILDYSLCQATWSKIQNKEA LTPIDISYLGPKNPGPGPAFTIINGTLHYFNTRYIRVDIAGPVTKEITGFVSGTSTSRVLWDQWFPYGENSIGPN GLLKTASGYKYPLFMVGTGVLDADIHKLGEATVIEHPHAKEAQKVVDDSEVIFFGDTGVSKNPVEVVEGWFSGWR SSLMSIFGIILLIVCLVLIVRILIALKYCCVRHKKRTIYKEDLEMGRIPRRA (SEQ ID NO: 15) VSV-G Alagoa Full length WT: MTPAFILCMLLAGSSWAKFTIVFPQSQKGDWKDVPPNYRYCPSSADQNWHGDLLGVNIRAKMPKVHKAIKADGWM CHAAKWVTTCDYRWYGPQYITHSIHSFIPTKAQCEESIKQTKEGVWINPGFPPKNCGYASVSDAESIIVQATAHS VMIDEYSGDWLDSQFPTGRCTGSTCETIHNSTLWYADYQVTGLCDSALVSTEVTFYSEDGLMTSIGRQNTGYRSN YFPYEKGAAACRMKYCTHEGIRLPSGVWFEMVDKELLESVQMPECPAGLTISAPTQTSVDVSLILDVERMLDYSL CQETWSKVHSGLPISPVDLGYIAPKNPGAGPAFTIVNGTLKYFDTRYLRIDIEGPVLKKMTGKVSGTPTKRELWT EWFPYDDVEIGPNGVLKTPEGYKFPLYMIGHGLLDSDLQKTSQAEVFHHPQIAEAVQKLPDDETLFFGDTGISKN PVEVIEGWFSNWRSSVMAIVFAILLLVITVLMVRLCVAFRHFCCQKRHKIYNDLEMNQLRR (SEQ ID NO: 16) VSV-G Alagoa ectodomain WT: KFTIVFPQSQKGDWKDVPPNYRYCPSSADQNWHGDLLGVNIRAKMPKVHKAIKADGWMCHAAKWVTTCDYRWYGP QYITHSIHSFIPTKAQCEESIKQTKEGVWINPGFPPKNCGYASVSDAESIIVQATAHSVMIDEYSGDWLDSQFPT GRCTGSTCETIHNSTLWYADYQVTGLCDSALVSTEVTFYSEDGLMTSIGRQNTGYRSNYFPYEKGAAACRMKYCT HEGIRLPSGVWFEMVDKELLESVQMPECPAGLTISAPTQTSVDVSLILDVERMLDYSLCQETWSKVHSGLPISPV DLGYIAPKNPGAGPAFTIVNGTLKYFDTRYLRIDIEGPVLKKMTGKVSGTPTKRELWTEWFPYDDVEIGPNGVLK TPEGYKFPLYMIGHGLLDSDLQKTSQAEVFHHPQIAEAVQKLPDDETLFFGDTGISKNPVEVIEGWFSNWRSSVM AIVFAILLLVITVLMVRLCVAFRHFCCQKRHKIYNDLEMNQLRR (SEQ ID NO: 17) VSV-G Cocal Full length WT: MNFLLLTFIVLPLCSHAKFSIVFPQSQKGNWKNVPSSYHYCPSSSDQNWHNDLLGITMKVKMPKTHKAIQADGWM CHAAKWITTCDFRWYGPKYITHSIHSIQPTSEQCKESIKQTKQGTWMSPGFPPQNCGYATVTDSVAVVVQATPHH VLVDEYTGEWIDSQFPNGKCETEECETVHNSTVWYSDYKVTGLCDATLVDTEITFFSEDGKKESIGKPNTGYRSN YFAYEKGDKVCKMNYCKHAGVRLPSGVWFEFVDQDVYAAAKLPECPVGATISAPTQTSVDVSLILDVERILDYSL CQETWSKIRSKQPVSPVDLSYLAPKNPGTGPAFTIINGTLKYFETRYIRIDIDNPIISKMVGKISGSQTERELWT EWFPYEGVEIGPNGILKTPTGYKFPLFMIGHGMLDSDLHKTSQAEVFEHPHLAEAPKQLPEEETLFFGDTGISKN PVELIEGWFSSWKSTVVTFFFAIGVFILLYVVARIVIAVRYRYQGSNNKRIYNDIEMSRFRK (SEQ ID NO: 18) VSV-G Cocal ectodomain WT: KFSIVFPQSQKGNWKNVPSSYHYCPSSSDQNWHNDLLGITMKVKMPKTHKAIQADGWMCHAAKWITTCDFRWYGP KYITHSIHSIQPTSEQCKESIKQTKQGTWMSPGFPPQNCGYATVTDSVAVVVQATPHHVLVDEYTGEWIDSQFPN GKCETEECETVHNSTVWYSDYKVTGLCDATLVDTEITFFSEDGKKESIGKPNTGYRSNYFAYEKGDKVCKMNYCK HAGVRLPSGVWFEFVDQDVYAAAKLPECPVGATISAPTQTSVDVSLILDVERILDYSLCQETWSKIRSKQPVSPV DLSYLAPKNPGTGPAFTIINGTLKYFETRYIRIDIDNPIISKMVGKISGSQTERELWTEWFPYEGVEIGPNGILK TPTGYKFPLFMIGHGMLDSDLHKTSQAEVFEHPHLAEAPKQLPEEETLFFGDTGISKNPVELIEGWFSSWKSTVV TFFFAIGVFILLYVVARIVIAVRYRYQGSNNKRIYNDIEMSRFRK (SEQ ID NO: 19) VSV-G Morreton Full length WT: -72- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT MLVLYLLLSLLALGAQCKFTIVFPHNQKGNWKNVPANYQYCPSSSDLNWHNGLIGTSLQVKMPKSHKAIQADGWM CHAAKWVTTCDFRWYGPKYVTHSIKSMIPTVDQCKESIAQTKQGTWLNPGFPPQSCGYASVTDAEAVIVKATPHQ VLVDEYTGEWVDSQFPTGKCNKDICPTVHNSTTWHSDYKVTGLCDANLISMDITFFSEDGKLTSLGKEGTGFRSN YFAYENGDKACRMQYCKHWGVRLPSGVWFEMADKDIYNDAKFPDCPEGSSIAAPSQTSVDVSLIQDVERILDYSL CQETWSKIRAHLPISPVDLSYLSPKNPGTGPAFTIINGTLKYFETRYIRVDIAGPIIPQMRGVISGTTTERELWT DWYPYEDVEIGPNGVLKTATGYKFPLYMIGHGMLDSDLHISSKAQVFEHPHIQDAASQLPDDETLFFGDTGLSKN PIELVEGWFSGWKSTIASFFFIIGLVIGLYLVLRIGIALCIKCRVQEKRPKIYTDVEMNRLDR (SEQ ID NO: 20) VSV-G Morreton ectodomain WT: KFTIVFPHNQKGNWKNVPANYQYCPSSSDLNWHNGLIGTSLQVKMPKSHKAIQADGWMCHAAKWVTTCDFRWYGP KYVTHSIKSMIPTVDQCKESIAQTKQGTWLNPGFPPQSCGYASVTDAEAVIVKATPHQVLVDEYTGEWVDSQFPT GKCNKDICPTVHNSTTWHSDYKVTGLCDANLISMDITFFSEDGKLTSLGKEGTGFRSNYFAYENGDKACRMQYCK HWGVRLPSGVWFEMADKDIYNDAKFPDCPEGSSIAAPSQTSVDVSLIQDVERILDYSLCQETWSKIRAHLPISPV DLSYLSPKNPGTGPAFTIINGTLKYFETRYIRVDIAGPIIPQMRGVISGTTTERELWTDWYPYEDVEIGPNGVLK TATGYKFPLYMIGHGMLDSDLHISSKAQVFEHPHIQDAASQLPDDETLFFGDTGLSKNPIELVEGWFSGWKSTIA SFFFIIGLVIGLYLVLRIGIALCIKCRVQEKRPKIYTDVEMNRLDR (SEQ ID NO: 21) -73- IPTS / 128954004.1
Claims
DOCKET NO: INH-032WO PATENT What is Claimed:
1. A method of determining the infectious titer of a pharmaceutical composition comprising a viral vector , wherein the viral vector comprises a nucleic acid molecule encoding for a chimeric antigen receptor comprising an antigen binding domain, the method comprising: contacting ex vivo an immune cell preparation comprising immune cells infected with the pharmaceutical composition comprising the viral vector with a first antibody and a second antibody, wherein the first antibody binds to an immune cell surface marker (ICSM) of interest on the infected immune cells and the second antibody is an idiotypic antibody that binds to the antigen binding domain of the chimeric antigen receptor to produce an antibody labeled immune cell preparation; and analyzing the antibody labeled immune cell preparation to determine the number of cells that are positive for the immune cell surface marker of interest (ICSM+) and positive for the antigen binding domain of the chimeric antigen receptor (CAR+) to determine the infectious titer of the pharmaceutical composition comprising the virus.
2. The method of claim 1, wherein the infectious titer is infectious transducing (infectious) units / mL (“IU”).
3. The method of claim 1, wherein the infectious titer is calculated by the following formula: IU=[(%CAR+ / ICSM+) x (Total number of cells seeded in well) x (Dilution Factor)] / (Total and cell volume(mL)); or= ^% cells CAR^^ x ^# cells plated^ x total dilution mL transduction volume ^mL^ 4. The method of claim 1, wherein the first antibody is labeled with a first label and the second antibody is labeled with a second label, wherein the first label and the second label are different.
5. The method of claim 1, wherein the analyzing is performed by flow cytometry to detect the cells that are ICSM+and CAR+.
6. The method of claim 1, wherein the analyzing comprises fixing the cells prior to -74- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT performing flow cytometry.
7. The method of claim 6, wherein fixing the cells comprises.
8. The method of claim 7, wherein fixing comprises fixing the cells in formaldehyde.
9. The method of claim 7, wherein fixing comprises fixing the cells in 3.7% formaldehyde in PBS (formalin).
10. The method of claim 1, wherein the method comprises infecting a population of cells with the pharmaceutical composition comprising the virus encoding for the chimeric antigen receptor to produce the immune cell preparation infected with the pharmaceutical composition.
11. The method of claim 11, wherein the viral vector is a lentivirus viral vector.
12. The method of claim 11, wherein the lentivirus viral vector is a pseudotyped lentivirus viral vector.
13. The method of claim 12, wherein the pseudotyped lentivirus is pseudotyped with VSV- G.
14. The method of claim 1, wherein the immune cells infected with the pharmaceutical composition are T cells.
15. The method of claim 14, wherein the T cells are CD7+cells.
16. The method of claim 1, wherein the first antibody specifically binds to CD7.
17. The method of claim 1, wherein the antigen binding domain of the CAR binds to CD19 or CD20.
18. The method of claim 17, wherein the second antibody specifically binds to the antigen binding domain that binds to CD20. -75- IPTS / 128954004.1DOCKET NO: INH-032WO PATENT 19. The method of claim 17, wherein the second antibody specifically binds to the antigen binding domain that binds to CD19.
20. A method of treating a disease in a subject with a pharmaceutical composition comprising a viral vector comprising a nucleic acid molecule encoding for a chimeric antigen receptor, the method comprising: determining the infectious titer according to any one of claims 1-19; and administering an effective amount of the pharmaceutical composition to the subject in an amount based on the determined infectious titer.
21. The method of claim 20, wherein the pharmaceutical composition is administered parenterally.
22. The method of any one of claims 1-21, wherein the viral vector is a lentiviral vector pseudotyped with a VSV-G polypeptide comprising a mutation that corresponds to a mutation at position 182 of SEQ ID NO:
2.
23. The method of claim 22, wherein the viral vector is a lentiviral vector pseudotyped with a VSV-G polypeptide comprising a mutation that corresponds to a mutation at position 182 of SEQ ID NO:
2.
24. The method of any one of claims 1-23, wherein the viral vector, such as a lentiviral vector, is pseudotyped with a VSV-G polypeptide comprising a mutation that corresponds to a mutation at position 182 of SEQ ID NO:
2. -76- IPTS / 128954004.1
Citation Information
Patent Citations
Pseudotyped viral particles, compositions comprising the same, and uses thereof
US11767366B1
Anti-idiotypic antibodies against Anti-CD19 antibodies
US20240018268A1