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`63/154,639
`02/26/2021
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`SEED INTELLECTUAL PROPERTY LAW GROUP LLP
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`CONFIRMATION NO. 6215
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`FILING RECEIPT
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`NV...
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`Date Mailed: 03/29/2021
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`It will not be examined for patentability and will
`Receipt is acknowledged ofthis provisional patent application.
`become abandoned notlater than twelve monthsafter its filing date. Any correspondence concerning the application
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`Inventor(s)
`
`Applicant(s)
`
`Molly R. Perkins, Milton, MA;
`Kevin M. Friedman, Melrose, MA;
`
`ViraLogic Therapeutics, Inc., Boston, MA
`Powerof Attorney:
`Eileen Sun--57270
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`Permission to Access Application via Priority Document Exchange: Yes
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`** SMALL ENTITY **
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`page 1 of 3
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`KELONIA EXHIBIT 1006
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`Page 1 of 109
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`KELONIA EXHIBIT 1006
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`

`

`Title
`
`LYMPHOCYTE TARGETED LENTIVIRAL VECTORS
`
`Statement under 37 CFR 1.55 or 1.78 for AIA (First Inventor to File) Transition Applications: No
`
`PROTECTING YOUR INVENTION OUTSIDE THE UNITED STATES
`
`Since the rights granted by a U.S. patent extend only throughout the territory of the United States and have no
`effect in a foreign country, an inventor who wishes patent protection in another country must apply for a patent
`in a specific country or in regional patent offices. Applicants may wish to consider the filing of an international
`application under the Patent Cooperation Treaty (PCT). An international (PCT) application generally has the same
`effect as a regular national patent application in each PCT-member country. The PCT process simplifies thefiling
`of patent applications on the same invention in member countries, but does not result in a grant of "an international
`patent" and doesnot eliminate the need of applicants to file additional documents and fees in countries where patent
`protection is desired.
`
`Almost every country has its own patent law, and a person desiring a patent in a particular country must make an
`application for patent in that country in accordance with its particular laws. Since the laws of many countries differ
`in various respects from the patent law of the United States, applicants are advised to seek guidance from specific
`foreign countries to ensure that patent rights are not lost prematurely.
`
`Applicants also are advised that in the case of inventions made in the United States, the Director of the USPTO must
`issue a license before applicants can apply for a patent in a foreign country. Thefiling of a U.S. patent application
`serves as a request for a foreign filing license. The application's filing receipt contains further information and
`guidance asto the status of applicant's license for foreign filing.
`
`Applicants may wish to consult the USPTO booklet, "General Information Concerning Patents” (specifically, the
`section entitled "Treaties and Foreign Patents") for more information on timeframes and deadlinesfor filing foreign
`patent applications. The guide is available either by contacting the USPTO Contact Center at 800-786-9199, or it
`can be viewed on the USPTOwebsite at http:/Awww.uspto.gov/web/offices/pac/doc/general/index.html.
`
`For information on preventing theft of your intellectual property (patents, trademarks and copyrights), you may wish
`to consult the U.S. Government website, http:/Awww.stopfakes.gov. Part of a Department of Commerceinitiative,
`this website includes self-help "toolkits" giving innovators guidance on howto protectintellectual property in specific
`countries such as China, Korea and Mexico. For questions regarding patent enforcement issues, applicants may
`call the U.S. Governmenthotline at 1-866-999-HALT(1-866-999-4258).
`
`LICENSE FOR FOREIGN FILING UNDER
`
`Title 35, United States Code, Section 184
`
`Title 37, Code of Federal Regulations, 5.11 & 5.15
`
`GRANTED
`
`if the phrase "IF REQUIRED, FOREIGN FILING
`The applicant has been granted a license under 35 U.S.C. 184,
`LICENSE GRANTED"followed by a date appears on this form. Such licenses are issuedin all applications where
`the conditions for issuanceof a license have been met, regardless of whether or not a license may be required as
`set forth in 37 CFR 5.15. The scope andlimitations of this license are set forth in 37 CFR 5.15(a) unless an earlier
`
`page 2 of 3
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`license has been issued under 37 CFR 5.15(b). The license is subject to revocation upon written notification. The
`date indicated is the effective date of the license, unless an earlier license of similar scope has been granted under
`37 GFR 5.13 or 5.14.
`
`This license is to be retained by the licensee and maybe used at any time onor after the effective date thereof unless
`it is revoked. This license is automatically transferred to any related applications(s)filed under 37 CFR 1.53(d). This
`license is not retroactive.
`
`The grantof a license doesnotin any way lessen the responsibility of a licensee for the security of the subject matter
`as imposed by any Government contract or the provisions of existing laws relating to espionage and the national
`security or the export of technical data. Licensees should apprise themselvesof current regulations especially with
`respect to certain countries, of other agencies, particularly the Office of Defense Trade Controls, Department of
`State (with respect to Arms, Munitions and Implements of War (22 CFR 121-128)); the Bureau of Industry and
`Security, Department of Commerce (15 CFR parts 730-774); the Office of Foreign AssetsControl, Department of
`Treasury (31 CFR Parts 500+) and the Departmentof Energy.
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`NOT GRANTED
`
`No license under 35 U.S.C. 184 has been granted atthis time, if the phrase "IF REQUIRED, FOREIGN FILING
`LICENSE GRANTED" DOES NOTappear on this form. Applicant maystill petition for a license under 37 CFR 5.12,
`if a license is desired before the expiration of 6 months from the filing date of the application. If 6 months has lapsed
`from the filing date of this application and the licensee has not received any indication of a secrecy order under 35
`U.S.C. 181, the licensee may foreign file the application pursuant to 37 CFR 5.15(b).
`
`
`SelectUSA
`
`The United States represents the largest, most dynamic marketplace in the world and is an unparalleled location for
`businessinvestment, innovation, and commercialization of new technologies. The U.S. offers tremendous resources
`and advantages for those who invest and manufacture goods here. Through SelectUSA, our nation works to
`promote andfacilitate business investment. SelectUSA provides information assistanceto the international investor
`community; serves as an ombudsmanfor existing and potential investors; advocates on behalf of U.S. cities, states,
`and regions competing for global investment; and counsels U.S. economic developmentorganizations on investment
`attraction best practices. To learn more about why the United States is the best country in the world to develop
`technology, manufacture products, deliver services, and grow your business, visit http://(www.SelectUSA.govor call
`+1-202-482-6800.
`
`page 3 of 3
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`LYMPHOCYTE TARGETED LENTIVIRAL VECTORS
`
`DETAILED DESCRIPTION
`
`Engineeredlentiviral vectors are described herein. The lentiviral vectors include
`
`a mutated, heterologous envelope protein, a targeting protein, and at least one
`
`transgenefor delivery to and expression by a cell characterized by the targeting protein.
`
`In some embodiments, the targeting protein is selected to target an immunecell,
`
`including, for example a lymphocyte or aT cell.
`
`In certain such embodiments, the
`
`lentiviral vectors described herein are capable of selectively targeting and efficiently
`
`transducing resting lymphocytes, e.g., T cells.
`
`Also provided are methods and materials for producing the lentiviral vectors
`
`described herein, methods for transducing target cells, and cells transduced by lentiviral
`
`vectors according to the present disclosure.
`
`In some embodiments, a lentiviral vector
`
`as described herein and/or cells transduced by such a vector may be usedin treating a
`
`disease or disorder responsive to the presenceof cells expressing the transgene
`
`delivered by the vector.
`
`Definitions
`
`Prior to setting forth this disclosure in more detail, it may be helpful to an
`
`understanding thereof to provide definitions of certain terms to be used herein.
`
`In the present description, any concentration range, percentage range, ratio
`
`range, or integer range is to be understood to include the value of any integer within the
`
`recited range and, when appropriate, fractions thereof (such as one tenth and one
`
`hundredth of an integer), unless otherwise indicated. Also, any number range recited
`
`herein relating to any physical feature, such as polymer subunits, size or thickness, are
`
`to be understood to include any integer within the recited range, unless otherwise
`
`indicated. As used herein, the term "about" means + 20% of the indicated range, value,
`
`or structure, unless otherwise indicated.
`
`It should be understood that the terms "a" and
`
`"an" as used herein refer to one or more" of the enumerated components. The use of
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`the alternative (e.g., "or") should be understood to meaneither one, both, or any
`
`combination thereof of the alternatives. As used herein, the terms "include," "have" and
`
`"comprise" are used synonymously, which terms and variants thereof are intended to be
`
`construed as non-limiting.
`
`Terms understood by thosein the art of antibody technology are each given the
`
`meaning acquired in the art, unless expressly defined differently herein. The term
`
`"antibody" is used in the broadest sense and includes polyclonal and monoclonal
`
`antibodies. An “antibody” mayrefer to an intact antibody comprising at least two heavy
`
`(H) chains and two light (L) chains inter-connected by disulfide bonds, as well as an
`
`antigen-binding portion (or antigen-binding domain) of an intact antibody that has or
`
`retains the capacity to bind a target molecule. An antibody may be naturally occurring,
`
`recombinantly produced, genetically engineered, or modified forms of immunoglobulins,
`
`for example intrabodies, peptibodies, nanobodies, single domain antibodies, SMIPs,
`
`multispecific antibodies (e.9., bispecific antibodies, diabodies, triabodies, tetrabodies,
`
`tandem di-scFv, tandem tri-scFv, ADAPTIR). A monoclonal antibody or antigen-binding
`
`portion thereof may be non-human, chimeric, humanized, or human, preferably
`
`humanized or human.
`
`Immunoglobulin structure and function are reviewed, for
`
`example, in Harlow et a/., Eds., Antibodies: A Laboratory Manual, Chapter 14 (Cold
`
`Spring Harbor Laboratory, Cold Spring Harbor, 1988). “Antigen-binding portion” or
`
`“antigen-binding domain” of an intact antibody is meant to encompassan “antibody
`
`fragment,” which indicates a portion of an intact antibody and refers to the antigenic
`
`determining variable regions or complementary determining regions of an intact
`
`antibody. Examples of antibody fragments include, but are not limited to, Fab, Fab’,
`
`F(ab’)2, and Fv fragments, Fab’-SH, F(ab’)2, diabodies, linear antibodies, scFv
`
`antibodies, VH, and multispecific antibodies formed from antibody fragments. A "Fab"
`
`(fragment antigen binding) is a portion of an antibody that binds to antigens and
`
`includes the variable region and CH1 of the heavy chain linked to the light chain via an
`
`inter-chain disulfide bond. An antibody maybe of any class or subclass, including IgG
`
`and subclasses thereof (IgG1,
`
`lgG2, IgGs, IgG), IgM, IgE, IgA, and IgD.
`
`The term "variable region" or "variable domain" in the context of an antibody
`
`refers to the domain of an antibody heavyorlight chain that is involved in binding of the
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`antibody to antigen. The variable domains (or regions) of the heavy chain and light
`
`chain (VH and VL, respectively) of a native antibody generally have similar structures,
`
`with each domain comprising four conserved framework regions (FRs) and three
`
`complementary determining regions (CDRs). (See, é.g., Kindt et al. Kuby Immunology,
`
`6th ed., W.H. Freeman and Co., page 91 (2007)). A single VH or VL domain may be
`
`sufficient to confer antigen-binding specificity. Furthermore, antibodies that bind a
`
`particular antigen may be isolated using a VH or VL domain from an antibody that binds
`
`the antigen to screen a library of complementary VL or VH domains, respectively. See,
`
`e.g., Portolano et al., J. Immunol. 150:880-887 (1993): Clarkson et al., Nature 352:624-
`
`628 (1991).
`
`The terms "complementarity determining region" and "CDR," which are
`
`synonymouswith "hypervariable region" or "HVR," are knownin the art to refer to non-
`
`contiguous sequences of amino acids within antibody variable regions, which confer
`
`antigen specificity and/or binding affinity.
`
`In general, there are three CDRsin each
`
`heavy chain variable region (HCDR1, HCDR2, HCDR3) and three CDRsin eachlight
`
`chain variable region (LCDR1, LCDR2, LCDR3).
`
`As used herein, the terms “binding domain’, “binding region”, and “binding
`
`moiety" refer to a molecule, such as a peptide, oligopeptide, polypeptide, or protein that
`
`possessesthe ability to specifically and non-covalently bind, associate, unite, recognize,
`
`or combine with a target molecule (e.g., tumor antigen). A binding domain includes any
`
`naturally occurring, synthetic, semi-synthetic, or recombinantly produced binding partner
`
`for a biological molecule or other target of interest.
`
`In some embodiments, the binding
`
`domain is an antigen-binding domain, such as an antibody or functional binding domain
`
`or antigen-binding portion thereof. Exemplary binding domainsinclude single chain
`
`antibody variable regions (e€.g., domain antibodies, sFv, scFv, Fab), receptor
`
`ectodomains (e.g., TNF-a), ligands (e.g., cytokines, chemokines), or synthetic
`
`polypeptides selected for the specific ability to bind to a biological molecule.
`
`"Major histocompatibility complex molecule" (MHC molecule) refers to a
`
`glycoprotein that delivers a peptide antigen to a cell surface. MHC class | molecules
`
`are heterodimers composed of a membrane spanning a chain (with three a domains)
`
`and a non-covalently associated 82 microglobulin. MHC class II molecules are
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`composedof two transmembrane glycoproteins, a and B, both of which span the
`
`membrane. Each chain has two domains. MHC class | molecules deliver peptides
`
`originating in the cytosol to the cell surface, where peptide: MHC complex is recognized
`
`by CD8* T cells. MHC classII molecules deliver peptides originating in the vesicular
`
`system to the cell surface, where they are recognized by CD4* T cells. An MHC
`
`molecule may be from various animal species, including human, mouse, rat, or other
`
`mammals.
`
`“Chimeric antigen receptor” (CAR) refers to a chimeric fusion protein comprising
`
`two or more distinct domainslinked together in a way that does not occur naturally in a
`
`host cell and can function as a receptor when expressed on the surface of a cell. CARs
`
`are generally composed of an extracellular domain comprising a binding domain that
`
`binds a target antigen, an optional extracellular spacer domain, a transmembrane
`
`domain, and an intracellular signaling domain (e.g., comprising an immunoreceptor
`
`tyrosine-based activation motif (ITAM)), and optionally an intracellular costimulatory
`
`domain).
`
`In certain embodiments, an intracellular signaling domain of a CAR has an
`
`ITAM (e.g., CD32) containing intracellular signaling domain and an intracellular
`
`costimulatory domain (é.g., 4-1BB).
`
`In certain embodiments, a CARis synthesized as a
`
`single polypeptide chain or is encoded by a nucleic acid molecule as a single chain
`
`polypeptide.
`
`A variety of assays are knownfor identifying binding domains of the present
`
`disclosure that specifically bind a particular target, as well as determining binding
`
`domain affinities, such as Western blot, ELISA, analytical ultracentrifugation,
`
`spectroscopy, surface plasmon resonance (BIACORE®)analysis, and MHC tetramer
`
`analysis (see also, e.g., Scatchard et a/., Ann. N.Y. Acad. Sci. 57:660, 1949; Wilson,
`
`Science 295:2103, 2002: Wolff et a/., Cancer Res. 53:2560, 1993: Altman ef al.,
`
`Science 274:94-96, 1996; and U.S. Patent Nos. 5,283,173, 5,468,614, or the
`
`equivalent). As used herein, "specifically binds" refers to an association or union of a
`
`binding domain, or a fusion protein thereof, to a target molecule with an affinity or Ka
`
`(i.e, an equilibrium association constant of a particular binding interaction with units of
`
`1/M) equal to or greater than 10° M, while not significantly associating or uniting with
`
`any other molecules or components in a sample.
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`The terms “antigen” and “Ag” refer to a molecule that is capable of inducing an
`
`immune response. The immune responsethatis induced may involve antibody
`
`production, the activation of specific immunologically-competent cells, or both.
`
`Macromolecules, including proteins, glycoproteins, and glycolipids, can serve as an
`
`antigen. Antigens can be derived from recombinant or genomic DNA. As contemplated
`
`herein, an antigen need not be encoded(i) solely by a full-length nucleotide sequence
`
`of a gene or(ii) by a “gene”at all. An antigen can be generated or synthesized, or an
`
`antigen can be derived from a biological sample. Such a biological sample can include,
`
`but is not limited, to a tissue sample, a tumor sample, a cell, or a biological fluid.
`
`The term "epitope" or "antigenic epitope" includes any molecule, structure, amino
`
`acid sequenceor protein determinant within an antigen that is specifically bound by a
`
`cognate immune binding molecule, such as an antibody or fragmentthereof (e.g., scFv),
`
`T cell receptor (TCR), CAR, or other binding molecule, domain or protein. Epitopic
`
`determinants generally contain chemically active surface groupings of molecules, such
`
`as amino acids or sugar side chains, and can have specific three-dimensional structural
`
`characteristics, as well as specific charge characteristics. An epitope may bealinear
`
`epitope or a conformational epitope.
`
`As used herein, an "effector domain" is an intracellular portion of a fusion protein
`
`or chimeric receptor that can directly or indirectly promote a biological or physiological
`
`response in a cell expressing the effector domain when receiving the appropriate signal.
`
`In certain embodiments, an effector domain is part of a protein or protein complex that
`
`receives a signal when bound.
`
`In other embodiments, the effector domain is part of a
`
`protein or protein complex that binds directly to a target molecule, which triggers a
`
`signal from the effector domain. For example, in response to binding of a CAR to a
`
`target molecule, the effector domain may transducea signal to the interior of the host
`
`cell, eliciting an effector function. An effector domain may directly promote a cellular
`
`response when it contains one or more signaling domains or motifs.
`
`In other
`
`embodiments, an effector domain will indirectly promote a cellular response by
`
`associating with one or more otherproteins that directly promote a cellular response.
`
`"Junction amino acids" or "junction amino acid residues" refer to one or more
`
`(e.g., about 2-20) amino acid residues between two adjacent motifs, regions or domains
`
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`of a polypeptide. Junction amino acids mayresult from the construct design of a
`
`chimeric protein (e.g., amino acid residues resulting from the use of a restriction
`
`enzyme site during the construction of a nucleic acid molecule encoding a fusion
`
`protein).
`
`A “disease”is a state of health of a subject wherein the subject cannot maintain
`
`homeostasis, and wherein, if the disease is not ameliorated, then the subject's health
`
`continues to deteriorate.
`
`In contrast, a “disorder” or “undesirable condition” in a subject
`
`is a State of health in which the subject is able to maintain homeostasis, but in which the
`
`subject’s state of health is less favorable than it would be in the absenceof the disorder
`
`or undesirable condition. Left untreated, a disorder or undesirable condition does not
`
`necessarily result in a further decreasein the subject’s state of health.
`
`“Nucleic acid molecule” and “polynucleotide” can be in the form of RNA or DNA,
`
`which includes cDNA, genomic DNA, and synthetic DNA. A nucleic acid molecule may
`
`be composed of naturally occurring nucleotides (such as deoxyribonucleotides and
`
`ribonucleotides), analogs of naturally occurring nucleotides (e.g., a-enantiomeric forms
`
`of naturally occurring nucleotides), or a combination of both. Modified nucleotides can
`
`have modifications in or replacement of sugar moieties, or pyrimidine or purine base
`
`moieties. Nucleic acid monomers can belinked by phosphodiester bonds or analogs of
`
`such linkages. Analogs of phosphodiester linkages include phosphorothioate,
`
`phosphorodithioate, phosphoroselenoate, phosphorodiselenoate,
`
`phosphoroanilothioate, phosphoranilidate, pnosphoramidate, and the like. A nucleic
`
`acid molecule may be double stranded or single stranded, and if single stranded, may
`
`be the coding strand or non-coding (anti-sense strand). A coding molecule may have a
`
`coding sequenceidentical to a coding sequence knownin the art or may have a
`
`different coding sequence, which, as the result of the redundancy or degeneracy of the
`
`genetic code, or by splicing, can encode the same polypeptide.
`
`“Encoding” refers to the inherent property of specific polynucleotide sequences,
`
`such as DNA, cDNA, and mRNAsequences, to serve as templates for synthesis of
`
`other polymers and macromoleculesin biological processes having either a defined
`
`sequenceof nucleotides(/.e., FRNA, tRNA and mRNA)or a defined sequence of amino
`
`acids andthe biological properties resulting therefrom. Thus, a polynucleotide encodes
`
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`a protein if transcription and translation of mRNA corresponding to that polynucleotide
`
`producesthe protein in a cell or other biological system. Both a coding strand and a
`
`non-coding strand can be referred to as encoding a protein or other product of the
`
`polynucleotide. 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.
`
`As used herein, the term "endogenous" or "native" refers to a gene, protein,
`
`compound, molecule or activity that is normally present in a host or host cell, including
`
`naturally occurring variants of the gene, protein, compound, molecule, or activity.
`
`As used herein, "homologous" or "homolog" refers to a molecule or activity from
`
`a hostcell that is related by ancestry to a second gene or activity, e.g., from the same
`
`host cell, from a different host cell, from a different organism, from a different strain,
`
`from a different species. For example, a heterologous molecule or heterologous gene
`
`encoding the molecule may be homologousto a native host cell molecule or gene that
`
`encodes the molecule, respectively, and may optionally have an altered structure,
`
`sequence, expression level or any combination thereof.
`
`As used herein, "heterologous" nucleic acid molecule, construct or sequence
`
`refers to a nucleic acid molecule or portion of a nucleic acid molecule that is not native
`
`to a host cell, but can be homologousto a nucleic acid molecule or portion of a nucleic
`
`acid molecule from the host cell. The source of the heterologous nucleic acid molecule,
`
`construct or sequence can be from a different genus or species.
`
`In some embadimerts,
`
`the heterologous nucleic acid molecules are not naturally occurring.
`
`In certain
`
`embodiments, a heterologous nucleic acid molecule is added (/.e., not endogenous or
`
`native) into a host cell or host genome by, for example, conjugation, transformation,
`
`transfection, transduction, electroporation, or the like, wherein the added molecule can
`
`integrate into the host cell genome or exist as extra-chromosomal genetic material (e.g.,
`
`as a plasmid or other form of self-replicating vector), and can be presentin multiple
`
`copies.
`
`In addition, "heterologous" refers to a non-native enzyme, protein or other
`
`activity encoded by a non-endogenous nucleic acid molecule introduced into the host
`
`cell, even if the host cell encodes a homologousprotein oractivity.
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`As used herein, the term "engineered,"
`
`"recombinant," “mutant,” “modified” or
`
`"non-natural" refers to an organism, microorganism, cell, nucleic acid molecule, or
`
`vector that has been modified by introduction of a heterologous nucleic acid molecule,
`
`or refers to a cell or microorganism that has been genetically engineered by human
`
`intervention—thatis, modified by introduction of a heterologous nucleic acid molecule,
`
`or refers to a cell or microorganism that has been altered such that expression of an
`
`endogenous nucleic acid molecule or gene is controlled, deregulated or constitutive,
`
`where such alterations or modifications can be introduced by genetic engineering.
`
`Human-generated genetic alterations can include, for example, modifications
`
`introducing nucleic acid molecules (which may include an expression control element,
`
`such as a promoter) encoding one or more proteins, chimeric receptors, or enzymes, or
`
`other nucleic acid molecule additions, deletions, substitutions, or other functional
`
`disruption of or addition to a cell's genetic material. Exemplary modifications include
`
`those in coding regions or functional fragments thereof heterologous or homologous
`
`polypeptides from a reference or parent molecule. Additional exemplary modifications
`
`include, for example, modifications in non-coding regulatory regions in which the
`
`modifications alter expression of a gene or operon.
`
`As used here, the term “transgene”refers to a gene or polynucleotide encoding a
`
`protein of interest (e.g., a CAR) whose expression is desired in a host cell and that has
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`been transferred by genetic engineering techniquesinto a cell. A transgene may
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`encode proteins of therapeutic interest as well as proteins that are reporters, tags,
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`markers, suicide proteins, etc. A transgene may be from a natural source, modification
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`of a natural gene, or a recombinant or synthetic molecule.
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`In certain embodiments, a
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`transgene is a componentof a vector.
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`The tern “overexpressed” or “overexpression” of an antigen refers to an
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`abnormally high level of antigen expression in a cell. Overexpressed antigen or
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`overexpression of antigen is often associated with a disease stafe, such as in
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`nematological malignancies and cells farming a solid tumor within @ specific tissue or
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`organ of a subject. Solid tumors or hematological malignancies characterized by
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`overexpression of a turnor antigen can be determined by standard assays known in the
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`art.
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`As used herein, the terms “peptide,” “polypeptide,” and “protein” are used
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`interchangeably, and refer to a compound comprised of amino acid residues covalently
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`linked by peptide bonds. A protein or septide must cortain al least iwo amino acids,
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`and no limitation is placed on the maximum number of amino acids thal can comprise a
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`protein's or peptide’s sequence, Polypeptides include any peptide or protein comprising
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`two or more amino acids joined to each other by peptide bonds. As used herein, the
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`term refers fo both short chains, which also commionly are referred to in the ari as
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`peptides, oligopeptides and cligormmers, for example, and to longer chains, which
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`generally are referred to in the art as croteins, of which there are many types.
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`“Polypeptides” inciude, for example, biclogically active fragments, substantially
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`homologous polypeptides, oligopeptides, harnodimers, heterodimers, variants of
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`polypeptides, modified polypeptides, derivatives, analogs, fusion proteins, among
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`others. The polypeptides include natural peptides, recombinant peptides, synthetic
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`peptides, or a combination thereof.
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`As used herein, the term “mature polypeptide’ or “mature protein’ refers to a
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`protein or polypeptide that is secreted or localized in the cell membrane or inside ceriain
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`cell organelles (é.g., the encoplasmic reticulum, golgi, or endosome) and includes a
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`partially cleaved N-ferminal signal sequence or does not include an N-terminal signal
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`sequence (/.é., ihe N-terminal signal sequence nas been entirely removed, such as by
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`an endogenous cleavage process, from the protein or polypeptide).
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`A’signal sequence’, also referred to as “signal peptide’, “leader sequence’,
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`“leader peptide’, “localization signal’ or “localization sequence’, is a short peptide
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`(usually 13-36 amino acids in jengin} present at the N-ierminus of newly synihesized
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`proteins that are destined for the plasma membrane or a secretory pathway. A signal
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`sequence typically cornprises a short stretch of hydrophilic, positively charged amino
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`acids at the N-terminus, a central hydrophobic domain of 5-15 residues, and a C-
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`terminal region with a cleavage site for a signal sequence.
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`In eukaryotes, a signal
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`sequence prompts translocation of ihe newly syninesized protein to the endaplasmic
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`reticulum where it is cleaved by the signal peptidase, creating a mature protein that then
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`proceeds ia its appropriate destination. The diversity of signal sequence length and
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`amine acid composition makes it difficult to precisely predict the cleavage site. For
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`polypeptide sequences disclosures herein, where a signal sequence is noted, the
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`polypeptide sequence absent the signal sequence or having a partial signal sequence is
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`also coniempiated.
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`The "percent identity" between two or more nucleic acid or amino acid
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`sequencesis a function of the numberof identical positions shared by the sequences
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`(.é., % identity = number of identical positions/total number of positions x 100), taking
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`into account the number of gaps, and the length of each gap that needs to be
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`introduced to optimize alignment of two or more sequences. The comparison of
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`sequences and determination of percent identity between two or more sequences can
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`be accomplished using a mathematical algorithm, such as BLAST and Gapped BLAST
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`programs at their default parameters (e.g., Altschul et a/., J. Mol. Biol. 275:403, 1990;
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`see also BLASTN at www.ncbi.nim.nih.gov/BLAST).
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`A "conservative substitution" is recognized in the art as a substitution of one
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`amino acid for another amino acid that has similar properties. Exemplary conservative
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`substitutions are well knownin the art (see, e.g., WO 97/09433, page 10, published
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`March 13, 1997; Lehninger, Biochemistry, Second Edition; Worth Publishers, Inc.
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`NY: NY (1975), pp.71-77; Lewin, Genes IV, Oxford University Press, NY and Cell Press,
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`Cambridge, MA (1990), p. 8).
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`The term "chimeric" refers to any nucleic acid molecule or protein that is not
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`endogenous and comprises a combination of sequencesjoined or linked together that
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`are not naturally found joined or linked together in