Filed herewith is a Sequence Listing (name: ABZ001SeqListing_ST25.txt; created: Dec. 13, 2016; sized: 27 KB). The content of that Sequence Listing is incorporated herein by reference in its entirety.
The present application relates generally to a novel diversification and maturation method for polypeptide libraries using a yeast-based expression system. More specifically, the yeast system disclosed facilitates the polypeptide library diversification, protein maturation and screening of binder proteins with modified affinity to another molecule.
Antibodies have been widely accepted for treatment of a variety of diseases, including cancer, arthritis and infectious diseases. Currently more than 300 monoclonal antibody-based drugs are in clinical trials. The predominant advantage of antibody-mediated therapy is its high specificity, facilitated by direct binding to the target(s) for neutralization or elimination (K
Success in generation of highly specific antibodies in an ex-vivo system depends on the ability to establish highly diverse heavy and light chain libraries together with efficient screening capacity. Currently ex-vivo non-mammalian approaches for generating antibodies such as phage display (H
In both prokaryotic and eukaryotic cells, there is a complex system that maintains genomic integrity, including e.g., the DNA polymerase complex copies DNA with high fidelity; the post-replication mismatch repair system repairs errors generated during replication; the DNA recombination machinery repairs DNA damage via homologous recombination, and the excision repair pathway corrects DNA adducts (B
For antibody maturation, it is preferred to have hypermutation caused by base substitutions as the latter do not cause shifts of the open reading frame. Substitution mutations in general are generated during DNA replication by nucleotide mis-incorporation either caused by infidelity of DNA polymerases, or by the presence of ambiguous nucleotide analogues (e.g. the nucleotide analog 6N-hydroxylamino purine can pair with either cytidine or thymine), or modification of the DNA template (e.g. Cytosine is deaminated to Uracil that in turn mimics Thymine pairing with Adenine). Cytosine-to-Uracil deamination occurs either spontaneously or by the action of cytosine deaminases (D
In mammals, the action of activation-induced deaminase (AID) is essential for functional antigen receptor maturation, by mediating class switching, gene conversion and hypermutation (for review see (K
Based on the mutator effect resulting from overexpression of human Activation-induced cytidine deaminase (AID) (P
Activation-induced cytidine deaminase (AID) and APOBEC (“apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like”) are members of the large and diverse cytidine deaminase family. Cytidine deaminases have been reported in various organisms including bacteria, yeast, tetrapods, jawless vertebrates and jawed vertebrates (R
The invention provided is a method and composition consisting of a highly engineered yeast mutator strain, expressing a jawless vertebrate sea lamprey cytidine deaminase as an active mutator gene, and grown in the presence of a mutation-inducing chemical, that together are used to diversify a library of polypeptides, that are cell surface accessible for binding to macromolecules. Jawless vertebrates have a fundamentally different immunological system compared to that of jawed vertebrates. Instead of immunoglobulins, the variable lymphocyte receptors (VLRs) of jawless fish are composed of highly diverse leucine-rich repeats (LRRs) (for review see (R
The expression of CDA1 in E. coli and yeast causes strong mutator phenotypes (R
There is a continuing need in the art for improving the generation of binding-specific antibodies or antibody analogs. This invention is a novel technology platform, called Self-Diversifying Antibody Library or SDALib that comprises a monoclonal antibody generating system providing a diverse array of complete antibodies in vitro, without using in vivo immunization. The invented system can be used for polypeptide library diversification, protein maturation and screening of binder proteins with modified affinity to another molecule. Advantages of this invention can include a low cost, rapid growth eukaryotic protein expression and surface display system with ease of culture and culture maintenance, facile manipulation and genetic engineering. Moreover, yeast mating allows random combination of antibody heavy chain and light chain libraries to form a combined library with highly diverse random H/L combinations. The expression of lamprey CDA—the most powerful deaminase mutator of DNA in yeast in combination with the chemical supermutagen HAP allows rapid library diversification. Finally the use of diploid and/or polyploid yeast strains versus the normally used haploid yeast version protect yeast cells from lethal mutation damage due to the presence of two or more copies of essential genes. In combination with panning and Fluorescence Assisted Cell Sorting (FACS) yeast cells expressing functional binders can be quickly identified and isolated.
The present invention provides a method and kit for diversifying a polypeptide library and selecting binders to a target of interest. In a preferred embodiment, methods and kits for isolating camelid single domain VHH antibodies are disclosed. In other embodiments, the cell-based self-diversifying methods are used to isolate human heavy-chain only single domain antibodies, human single chain variable fragments (ScFv) and human traditional antibodies. The cell-based self-diversifying platform has additional applications in diversifying other binders and maturating binders to modulate their functional activity.
In an exemplary embodiment of the invention, influenza H5N1 neuraminidase is presented as an antigen of interest. Genetically engineered host cells comprising a self-diversifying surface display camelid VHH antibody library are then contacted with the antigen target. The engineered cells expressing antibodies reactive to the antigen is enriched by biological panning and isolated by Fluorescence-Activated Cell Sorting or FACS. Antibodies from sorted cells are purified and confirmed for the target-specific binding activity.
In another embodiment of the invention, a cell-based system for protein binder discovery is provided, wherein the system comprises a) a first DNA construct comprising a nucleic acid molecule encoding a protein scaffold operably linked to a promoter and a DNA motif; b) a second DNA construct having a nucleic acid molecule encoding a second polypeptide operably linked to a promoter; c) diversifying cell culture media supplemented with protein-expression inducer and mutation-causing chemicals; and d) Two yeast strains of opposite mating types; the first yeast strain contains said first DNA construct; the second yeast strain contains said second construct; the final host cell formed by mating the first and the second yeast strains comprising said first and second DNA constructs, diversification of said protein scaffold in said host cell being dependent upon enzymatic activity of said second polypeptide or the presence of the mutation-causing chemicals supplemented in said cell culture media.
In yet another embodiment, a method for isolating binders to a target of interest with modulated binding activity is provided, wherein the method comprises: a) providing a host cell containing a first DNA construct comprising a nucleic acid molecule encoding a protein scaffold operably linked to a first promoter and a DNA recognition sequence; a second DNA construct having a nucleic acid molecule encoding a second polypeptide operably linked to a second promoter; and diversifying cell culture media supplemented with protein-expression inducers and mutation-causing chemicals; b) culturing said host cells in said diversifying media to diversify the said binder encoding genes; and c) isolating host cell expressing scaffold reactive to a target by either biological panning or FACS.
In a particular embodiment, the first DNA construct encodes a scaffold selected from the group of immunoglobulin heavy chain or light chain variable regions or polypeptide scaffolds including, but not limited to Anticalins, fibronectin type III domain—Adnectins, Designed Ankyrin Repeat Protein or DARPins and Centyrins. In a particular embodiment, the second DNA construct encodes cytidine deaminases selected from group of sea lamprey cytidine deaminase 1 (PmCDA1), chimeric cytidine deaminase CDA2/CDA1 and their variants.
So that the manner in which the above recited features of the present invention can be understood in detail, a more particular description of the invention, briefly summarized above, may be had by reference to embodiments, some of which are illustrated in the appended drawings. It is to be noted, however, that the appended drawings illustrate only illustrative embodiments of this invention and are therefore not to be considered limiting of its scope, for the invention may admit to other equally effective embodiments.
The Sequence Listing filed with this application as a text file includes the following protein sequences:
To facilitate understanding, identical reference numerals have been used, where possible, to designate comparable elements that are common to the figures. The figures are not drawn to scale and may be simplified for clarity. It is contemplated that elements and features of one embodiment may be beneficially incorporated in other embodiments without further recitation.
In accordance with the present invention, compositions, methods and kits are provided for polypeptide diversification and isolation of a binder protein to a target of interest. A yeast-based system is disclosed to produce protein scaffolds reactive to a target. In a preferred aspect of the invention, an antibody discovery method is provided which enables isolating target-specific antibodies starting from a naïve antibody library.
The following definitions are provided to facilitate an understanding of the present invention.
A “promoter” is a DNA sequence located proximal to the start of transcription at the 5′ end of an operably linked transcribed sequence. The promoter can contain one or more regulatory elements or modules that act together in coordinating and regulating transcription of the operably linked gene. An inducible promoter is a promoter that responds to the presence of different biochemical stimuli. Such promoters include, but are not limited, to the CUP1 promoter, heat shock promoters, galactose-inducible promoters, glycolytic promoters such as alcohol dehydrogenase (ADH) glyceraldehyde phosphate dehydrogenase (GPD) and the like.
“Operably linked” describes two macromolecular elements arranged such that modulating the activity of the first element induces an effect on the second element. In this manner, modulation of the activity of a promoter element can be used to alter and/or regulate the expression of an operably linked coding sequence. For example, the transcription of a coding sequence that is operably linked to a promoter element is induced by factors that “activate” the promoter's activity; transcription of a coding sequence that is operably-linked to a promoter element is inhibited by factors that “repress” the promoter's activity. Thus, a promoter region is operably linked to the coding sequence of a protein if transcription of such coding sequence activity is influenced by the activity of the promoter.
“Fusion construct” refers generally to recombinant genes which encode fusion proteins. Such fusion constructs can include operably linked nucleic acids isolated from two or more different genes.
A “fusion protein” is a hybrid protein, i.e., a protein that has been constructed to contain domains from at least two different proteins. An exemplary fusion protein, as described herein is a hybrid protein which possesses (a) a transcriptional regulatory domain from a transcriptional regulatory protein, or (b) a DNA binding domain from a DNA binding protein linked to a heterologous protein to be assayed for interaction. The structure of the fusion protein is such that the transcriptional regulatory domain and the DNA binding domain are arranged in a manner that allows both domains to be biologically active. The protein that is the source of the transcriptional regulatory domain is different from the protein that is the source of the DNA binding domain. In other words, the two domains are heterologous to each other. The transcriptional regulatory domain of the fusion protein can either activate or repress transcription of target genes, depending on the native biological activity of the domain.
The term “fusion protein gene” refers to a DNA sequence that encodes a fusion protein. A fusion protein gene can further provide transcriptional and translational regulatory elements for the transcriptional and translational control thereof.
A nucleic acid molecule, such as a DNA or gene is said to be “capable of expressing” a polypeptide if the molecule contains the coding sequences for the polypeptide operably linked to expression control sequences (e.g., promoter sequence) which, in the appropriate host environment, facilitate transcription, processing and translation of the encoded genetic information into a protein product.
The phrase “consisting essentially of” when referring to a particular nucleotide or amino acid means a sequence having the properties of a given reference sequence. For example, when used in reference to an amino acid sequence, the phrase includes the sequence per se and molecular modifications that would not affect the basic and novel characteristics of the sequence.
As used herein, a “cloning vector” is any entity that is capable of delivering a nucleic acid sequence into a host cell for cloning purposes. Examples of cloning vectors include plasmids or phage genomes. A plasmid which replicates autonomously in a host cell is especially preferred. Alternatively, a nucleic acid molecule which stably integrates into the host cell's chromosomal DNA and is inherited by daughter cells can be employed. Optionally, such vectors include a number of endonuclease recognition sites to facilitate manipulation of the sequence in a controlled and targeted fashion. Cloning vectors of the invention can also comprise sequences conferring resistance to selection agents, often referred to herein as selectable marker genes. For example, “a marker gene” can be a gene which confers resistance to a specific antibiotic on a host cell.
As used herein, an “expression vector” is a vehicle or vector similar to the cloning vector but is especially designed to provide an environment that facilitates expression of the cloned gene product after transformation into the host. Such vectors contain regulatory elements for expression in prokaryotic and/or eukaryotic hosts as well as sequences conferring selection properties of cells containing the expression vector. Optionally, enhancer elements, termination sequences, tissue-specificity elements, and/or translational initiation and termination sites can be included.
A “host” refers to any organism or cell line that is the recipient of a cloning or expression vector. In preferred embodiments, the host of the invention is a yeast cell or a cultured animal cell such as a mammalian or insect cell. Especially preferred is the yeast host Saccharomyces cerevisiae.
A “transformed cell” is any cell into which (or into an ancestor of which) exogenous DNA has been introduced by means of recombinant DNA techniques or cell fusion, e.g. mating.
“Response elements” are specific DNA sequences located in promoters of inducible genes; such inducers can include chemicals, hormones, metals such as zinc, cadmium or copper, temperature changes (e.g. heat shock) and transcription factors. In many instances, nuclear receptors in the form of homodimers, heterodimers or monomers bind specifically to DNA response elements to activate or repress transcription of the targeted genes in the presence or the absence of ligands for the nuclear receptors.
The terms “variant” or “derivative” in relation to lamprey CDA1 polypeptide includes any substitution of, variation of, modification of, replacement of, deletion of or addition of one (or more) amino acids from or to the polypeptide sequence of CDA1. Preferably, nucleic acids encoding CDA1 are understood to comprise variants or derivatives thereof.
Such “modifications” of CDA1 polypeptides include fusion proteins in which CDA1 polypeptide or a portion or fragment thereof is linked to or fused to another polypeptide or molecule.
The term “homologue” as used herein with respect to the nucleotide sequence and the amino acid sequence of CDA1 can be synonymous with allelic variations in the CDA1 sequences and includes known homologues.
The “functional activity” of a protein in the context of the present invention describes the function the protein performs in its tested environment. Altering or modulating the functional activity of a protein includes within its scope increasing, decreasing or otherwise altering the native activity of the protein itself. In addition, it also includes within its scope increasing or decreasing the level of expression and/or altering the intracellular distribution of the nucleic acid encoding the protein, and/or altering the intracellular distribution of the protein itself. By “cytidine deaminase mutation activity” or “mutator activity” is meant the functional activity of cytidine deaminase or its homologues to increase mutation above background without the presence of the enzyme.
The term “expression” refers to the transcription of a gene's DNA template to produce the corresponding mRNA and translation of this mRNA to produce the corresponding gene product (i.e., a peptide, polypeptide, or protein). The tem “activates gene expression” refers to inducing or increasing the transcription of a gene in response to a treatment where such induction or increase is compared to the amount of gene expression in the absence of said treatment. Similarly, the terms “decreases gene expression” or “down-regulates gene expression” refers to inhibiting or blocking the transcription of a gene in response to a treatment and where such decrease or down-regulation is compared to the amount of gene expression in the absence of said treatment.
The “mutation rate” is the rate at which a particular mutation occurs, usually given as the number of events per gene per generation whereas “mutation frequency” is the frequency at which a particular mutant is found in the population.
“Hypermutation” or “increased mutation rate” or “increased mutation frequency” refers to the mutation of a nucleic acid in a cell at a rate above background. Preferably, hypermutation refers to a rate of mutation of between 10−5 to 10−3/base/generation. This is greatly in excess of background mutation rates, which are of the order of 10−9 to 10−10/base/generation (D
The term “constitutive hypermutation” refers to the ability of certain cell lines to cause alteration of the nucleic acid sequence of one or more specific sections of endogenous or transgene DNA in a constitutive manner, that is without the requirement for external stimulation. Generally, such hypermutation is directed. In cells capable of directed constitutive hypermutation, sequences outside of the specific sections of endogenous or transgene DNA are not subjected to mutation rates above background mutation rates. The sequences which undergo constitutive hypermutation are under the influence of hypermutation-recruiting elements, as described further below, which direct the hypermutation to the locus in question. Thus in the context of the present invention, target nucleic acid sequences, into which it is desirable to introduce mutations, can be constructed, for example by replacing V gene transcription units in loci which contain hypermutation-recruiting elements with another desired transcription unit, or by constructing artificial genes comprising hypermutation-recruiting elements.
A wide variety of proteins have been subject to random mutation procedures to generate proteins that selectively bind substances. Those of skill will recognize proteins with a reasonable potential for generating such binding. As with many antibodies, scaffold proteins can be composed of subunit proteins. These are “scaffold proteins.” Scaffold proteins that have been used in the past include without limitation immunoglobulin heavy chain or light chain variable regions, combinations of light and heavy chains including Fab fragments, Anticalins, fibronectin type III domain (e.g., Adnectins), Designed Ankyrin Repeat Protein (DARPins), Centyrins, and the like.
A “scaffold protein library” is a library of genetically diverse scaffold proteins. For example, the library can encode Adnectins.
The cytidine deaminase used in the yeast cell embodiments is “effective to contribute to a mutagenic process for inducing a library of binding scaffold proteins from the yeast cell.” This means that, where used alone or in combination with other mutation-inducing circumstances, the cytidine deaminase contributes a statistically meaningful increase in creating binding scaffold protein mutant DNAs.
A surface, such as for example in a polystyrene multititer plate, has a substance “bound” thereto if its association with the surface is strong enough to allow cell panning. The binding can be, but is not necessarily, covalent.
A “color marker” has optical density (in a frequency band) or fluorescence directly, has enzymatic activity that generates the same, or is adapted to selectively bind one or more substances (e.g., biotin) such that eventually in the binding tree substances directly have or enzymatically generate optical density or fluorescence.
The meaning for “identity” for polypeptides is as follows: Polypeptide embodiments (including as components of methods or yeast cell systems) further include an isolated polypeptide comprising a polypeptide having at least about 50, 60, 70, 80, 85, 90, 95, 97 or 100% identity to a polypeptide “Reference Sequence” (e.g. SEQ ID NOs:1, 2, 3, 4 or 5), wherein said polypeptide sequence may be identical to the Reference Sequence or may include up to a certain integer number of amino acid alterations as compared to the Reference Sequence, wherein said alterations are selected from the group consisting of at least one amino acid deletion, substitution, including conservative and non-conservative substitution, or insertion, and wherein said alterations may occur at the amino- or carboxy-terminal positions of the Reference Sequence or anywhere between those terminal positions, interspersed either individually among the amino acids in the Reference Sequence or in one or more contiguous groups within the Reference Sequence, and wherein said number of amino acid alterations is determined by multiplying the total number of amino acids in the Reference Sequence by the integer defining the percent identity divided by 100 and then subtracting that product from said total number of amino acids in the Reference Sequence, or:
n
a
<x
a−(xa·y),
wherein na is the number of amino acid alterations, xa is the total number of amino acids in the Reference Sequence, y is 0.50 for 50%, 0.60 for 60%, 0.70 for 70%, 0.80 for 80%, 0.85 for 85%, 0.90 for 90%, 0.95 for 95%, 0.97 for 97% or 1.00 for 100%, and is the symbol for the multiplication operator, and wherein any non-integer product of xa and y is rounded down to the nearest integer prior to subtracting it from xa.
By way of example, a polypeptide sequence of the present invention may include a contiguous segment of sequence that is identical to the Reference Sequence, that is it may be 100% identical, or it may include up to a certain integer number of amino acid alterations as compared to the Reference Sequence such that the percent identity is less than 100% identity.
All ranges recited herein include ranges therebetween, and can be inclusive or exclusive of the endpoints. Optional included ranges are from integer values therebetween (or inclusive of one original endpoint), at the order of magnitude recited or the next smaller order of magnitude. For example, if the lower range value is 0.2, optional included endpoints can be 0.3, 0.4, . . . 1.1, 1.2, and the like, as well as 1, 2, 3 and the like; if the higher range is 8, optional included endpoints can be 7, 6, and the like, as well as 7.9, 7.8, and the like. One-sided boundaries, such as 3 or more, similarly include consistent boundaries (or ranges) starting at integer values at the recited order of magnitude or one lower. For example, 3 or more includes 4 or more, or 3.1 or more. If there are two ranges mentioned, such as about 1 to 10 and about 2 to 5, those of skill will recognize that the implied ranges of 1 to 5 and 2 to 10 are within the invention.
Cost effective and accelerated methods for antibody discovery will have broad impact on developing diagnostic, research and therapeutic antibodies. Currently ex-vivo non-mammalian approaches for generating antibodies such as phage display (HAWKINS et al. 1992), yeast surface display (B
Methods that can be potentially useful for antibody discovery are set forth in Table 1.
Numerous techniques to generate antibodies were evaluated. As can be seen from Table 1 only SDALib technology described herein meets the desired criteria of cost, speed, self-maturation, no antigen limitation and ease of application. While a number of in vitro techniques can generate antibody, for maturation they require additional steps including in vitro error-prone PCR and library sub-cloning. Antibody maturation by error-prone PCR followed by sub-cloning is easily doable if the antibody is expressed by a single gene such as in the single domain (human VH or camelid VHH) or in the single-chain variable fragment (scFv) formats. When antibodies consist of separate light and heavy chain genes, error-prone PCR sub-libraries have to be constructed for each antigen-specific clone to maintain heavy-light chain pairing. Otherwise random pairing of a light chain from one active antibody with a heavy chain from a different clone will not likely generate again a target-specific antibody.
There is a continuing need in the art for better developing antibodies. This invention is a novel technology platform, called Self-Diversifying Antibody Library or SDALib, that comprises a binding moiety (such as a monoclonal antibody) generating system providing a diverse array of binding moieties (such as complete antibodies) in vitro, without using immunization. The invented system can be used for polypeptide library diversification, protein maturation and screening of binder proteins with modified affinity to another molecule. Advantages of this invention include low cost, rapid growth eukaryotic protein expression and a surface display system with ease of culture, culture maintenance, facile manipulation and genetic engineering. Moreover, yeast mating allows combination of antibody heavy chain and light chain libraries to form a single library with highly diverse random H/L combinations. The expression of sea lamprey CDA—the most powerful deaminase mutator in yeast-directed to a DNA target in combination with the chemical supermutagen HAP allows rapid library diversification, and finally the use of diploid and/or polyploid yeast strains protect yeast cells from detrimental genetic damage of the induced mutagenesis due to the presence of two or more copies of essential genes. In combination with Fluorescence Assisted Cell Sorting (FACS) yeast cells expressing functional binders can be quickly identified.
In accordance with the present invention, a yeast-based genetic system and methods of use, thereof are provided to facilitate antibody discovery. The methods provided herein enable the rapid and efficient maturating and isolating antibody clones to an antigen target of interest starting from a naïve antibody library or to improve the activity of a known protein, including antibodies.
Nucleic acid molecules encoding the expression vectors of the invention can be prepared by two general methods: (1) They can be synthesized from appropriate chemical starting materials, or (2) they can be isolated from biological sources. Both methods utilize protocols well known in the art.
The availability of nucleotide sequence information, for the sea lamprey CDA1, as well as for secretory signals from alpha-mating factor or yeast SUC2 gene facilitates synthesis of DNA constructs containing such sequences. Synthetic oligonucleotides can be prepared by the phosphoramadite method employed in the Applied Biosystems 38A DNA Synthesizer or similar devices. The resultant construct can be purified according to methods known in the art, such as high performance liquid chromatography (HPLC). Long, double-stranded polynucleotides, such as a DNA molecule encoding a construct of the present invention, must be synthesized in stages due to the size limitations inherent in current oligonucleotide synthetic methods. Thus, for example, a 3 kilobase double-stranded molecule can be synthesized as several smaller segments of appropriate complementarity. Complementary segments thus produced can be ligated such that each segment possesses appropriate cohesive termini for attachment of an adjacent segment. Adjacent segments can be ligated by annealing cohesive termini in the presence of DNA ligase to construct the entire 3 kilobase double-stranded molecule. A synthetic DNA molecule so constructed can then be cloned and amplified in an appropriate vector. In alternative embodiments of the invention, the sea lamprey CDA1, yeast AGA2, yeast SUC2 secretory signal and camelid VHH genes can be substituted with similar genes with functional homology from other biological sources. In the PmCDA1 example, suitable candidate genes for such substitution include, without limitation, lamprey cytidine deaminase mutated (modified or altered cytidine deaminases), derivatives such as a CDA1 hybrid with ER DNA binding domain (ER-DBD), which also has high mutator phentotype once expressed in yeast defective in Uracil-DNA glycosylase. In addition, one can replace PmCDA1 with cytidine deaminase from other species, including but not limited to human AID.
Yeast SUC2 secretory signal of the invention used for promoting protein secretion can be derived from different species not limited to S. pombe and K. lactis. It can be substituted with yeast alpha mating factor secretory signal that also functions as secretory signal.
Similarly, the DNA binding domain of human estrogen alpha receptor (ER) of the invention can be derived from different species. The ER DNA binding domain has been used in the studies described herein. However, ER DNA binding domain (ER-DBD) from rat or mouse can have altered properties that can make them more robust and efficient than the human ER-DBD. The purpose of using ER-DBD fused with CDA is to recruit CDA to the ERE response sequence that is operably linked to VHH encoding genes. Thus, in this situation, the functional activity of ER-DBD can be replaced with other DNA binding domains to recruit CDA to a respective response element.
The interaction between a DNA binding domain and a DNA binding protein recognition sequence can be used to direct lamprey cytidine deaminase to a specific nucleic acid sequence. One way of directing mutation in this way is described as follows: an expression construct for expressing a fusion protein comprising lamprey cytidine deaminase with the estrogen receptor DNA binding domain (ERD) is created. The expression construct is expressed in yeast. The yeast host cell is also engineered such that the desired target gene is also operably linked to a short ERD recognition sequence. Those of skill will recognize that other DNA-binding moieties can be used to provide localization. A useful binding moiety is an ERDBD with about 85% or more sequence identity with the human ERDBD of SEQ ID NO. 14, or with about 90 or 95% or more sequence identity with one of SEQ ID NOs. 10, 11, 12 or 14.
Nucleic acid sequences encoding the components of the expression plasmids of the invention can be isolated from appropriate biological sources using methods known in the art. For example, RNA isolated from a mammalian or insect cell can be used as a suitable starting material for the generation of cDNA molecules encoding the different receptor proteins.
In accordance with the present invention, nucleic acids having the appropriate level of sequence homology with the protein coding region of the DNA molecules of the present invention can be identified by using hybridization and washing conditions of appropriate stringency. For example, hybridizations can be performed at 37° C. to 42° C. for at least six hours. Targets with greater than about 75% sequence identity would be observed using a hybridization temperature of 42° C. Such a sequence would be considered substantially homologous to the sequences of the present invention.
The nucleic acids of the invention can also be used as starting materials for the generation of sequence variants or truncation mutants of the nucleic acids of the invention using any number of synthetic and molecular biologic procedures well known in the art including, but not limited to, truncation at available restriction sites and site-directed mutagenesis techniques. Particular mutations can give rise to receptor proteins with altered characteristics such as increased or decreased ligand binding activity.
In one embodiment of the invention, the antibodies of the invention are expressed in yeast as fusion proteins having yeast secretory signal at the N-terminus. Secretory signal fusion at the N-terminus of the protein facilitates extracellular secretion of the protein following translation. After translation of recombinant proteins, the secretory signals at the N-terminus are cleaved by the host secretory pathway proteases and native proteins are released. It is widely known that the presence of the secretory signals results in secretion of proteins of interest in yeast (K
In embodiments of the invention, the antibodies of the invention are expressed in yeast as fusion proteins with yeast membrane anchor protein AGA2 at their C-termini. The protein membrane anchor functions to retain secreted antibodies or polypeptides on the yeast cell surface (B
In embodiments of the invention, the antibodies of the invention are expressed in yeast as ER-DBD fusion proteins. ER-DBD fusion can enhance but is not necessary for hypermutation in antibody-encoding DNA regions coupled with a ER-DBD response element (ERE).
In yet another embodiment of the invention, assays are provided wherein intact cells expressing a protein of interest are grown in cell culture media containing nucleotide base analogue molecules and molecules to induce expression of cytidine deaminase. After a suitable time period, the diversification of a gene or protein of interest is measured. Such diversification of a gene or protein of interest can be quantitated in any number of ways. For example, such cell systems can utilize a reporter system in which the production of the reporter signal is dependent on enzymatic or fluorescence or binding activity of the protein of interest. Numerous reporters can serve equally well in this application including but not limited to, beta-galactosidase, alkaline phosphatase, fluorescent green protein, antibody, protein scaffold and the like. Inactivation or activation of the gene of interest can be also measured as forward and reverse mutation rates. For example, mutation in the arginine permease encoding gene CAN1 confers resistance to canavanine (L
Assays for screening binders to a target of interest are also provided. Diversification of binders in the cell-based system can be followed by isolation of cells expressing modified binders reactive to a target by means of biological panning or fluorescence-activation cell sorting (FACS). Isolation of binders reactive to a target of interest can be performed as described previously (C
The following protocols are provided to facilitate construction of the expression plasmids for use in the methods and kits of the present invention.
Standard yeast and E. coli media were prepared as described in detail (C
Yeast strains suitable for use in the present invention include the yeast strains of opposite mating types A101: MatA ura3-52 trp1Δ63 leu2 pep4-3 prb1-22 prc1-407 ung1::HygB ham1::KanMX; A169: Mat Alpha Gal1p-AGA1::URA3 ura3-52 trp1::NatMX leu2-Δ200 his3-Δ200 lys2Δ pep4::ZeoR prbΔ1.6R can1 ung1::HygB ham1::KanMX and A170: MatA Gal1p-AGA1::URA3 ura3-52 trp1-Δ63 Gal1p-PmCDA1::LEU2 leu2 his3::zeoR pep4-3 prb1-22 prc1-407 ung1::HygB ham1::KanMX.
A series of yeast expression plasmids pESCLEU-PmCDA1, pESCLEU-PmCDA2, pESCLEU-PmCDA2/1 and pESCLEU-hAID have been constructed for expressing sea lamprey cytidine deaminases and their derivatives as well as human AID based on the pESCLEU plasmid backbone (Agilent Technologies).
A series of yeast expression plasmids for expression and display of a protein of interest on the yeast cell surface were constructed based on the yeast-E. coli single copy plasmid pRS314 (S
When a protein of interest is a heterodimer such as an antibody Fab fragment, it requires two plasmids to express both partners simultaneously. For example, to express and display antibody Fab fragments, two yeast-E. coli centromeric plasmids have to be constructed to express both heavy chain and light chains. For expression of heavy chain, the yeast-E. coli centromeric plasmid pRS314-Gal1/10p-EagI-SalI plasmid (
To display and diversify Fab fragments, heavy chain and light chain variable domains are cloned in frame at the cloning sites in the respective vectors described above. Heavy chain vectors are introduced into the A169 yeast strain by yeast transformation selecting colonies growing in media without tryptophan. Light chain vectors are introduced into the A170 strain that already contains the integrated PmCDA1 vector (
Also provided is a camelid VHH library constructed using the yeast-E. coli expression vector pRS314-Gal1/10-VHH (
A diploid host cell containing a first DNA construct having a nucleic acid molecule encoding a protein that is subjected for diversification and a second DNA construct having a nucleic acid molecule encoding cytidine deaminase will undergo diversification by two means either performed separately or in combination.
In the first means of diversification a host cell containing constructs of the invention is continuously grown in yeast selective media that contains promoter inducers including but not limited to (1) galactose (20 g/L) as a sole carbon source to induce the Gal1/10 promoter or (2) copper at concentrations of 100 micro molar to 1 mM to induce the Cup1 promoter. Under such conditions cytidine deaminase is expressed. Produced cytidine deaminases will convert C to U via deamination in transcriptionally active genes including a gene of interest.
In the second means of diversification, a host cell containing constructs of the invention is continuously grown in yeast selective media containing base analogues including, but not limited to 6N-hydroxylamine purine or HAP. During replication the base analog 6-N-hydroxylaminopurine (HAP) induces bidirectional GC->AT and AT->GC transitions (S
As gene diversification occurs via hypermutation that is active during cell division via DNA replication, the level of diversification obtained is directly related to numbers of mutations in a gene of interest that accumulate as cells grow. Therefore the longer cells undergo diversification, the more mutations will accumulate.
Specific embodiments according to the methods of the present invention will now be described in the following examples. The examples are illustrative only, and are not intended to limit the remainder of the disclosure in any way.
Where a sentence states that its subject is found in embodiments, or in certain embodiments, or in the like, it is applicable to any embodiment in which the subject matter can be logically applied.
Isolation of VHH Antibody Clones from a Naïve VHH Antibody Library
In accordance with the present invention, compositions and methods are provided for diversification of a polypeptide library and isolation of binders from a diversified polypeptide library to a target of interest. It has previously been demonstrated that the overexpression of sea lamprey CDA1 can cause mutations in yeast strains defective in Uracil DNA-glycosylase (UNG1 mutant) (M
Using prior art, mRNA from camelid blood leukocytes have been isolated, converted into cDNA and DNA regions encoding camelid immunoglobulin heavy chain variable domains have been cloned at the SfiI-SfiI sites of the vector in frame with secretory signal and the membrane anchor AGA2 as presented in the
The diploid VHH library underwent repeated diversification induction by continuous propagation at 20° C. for 24 hours in yeast buffered-media SGRCAA selective media (C
DNA Sequence Analysis of Isolated VHH Antibody Clones
Total plasmid DNA from a pool of FACS-sorted yeast cells was isolated and VHH encoding genes were PCR amplified for subsequent recloning into the pET22 (b) expression vector and the resulting individual E. coli clones were analyzed for anti-influenza H5N1 neuraminidase (“N1 NA”) activity. Protein expression was induced using autoinduction media as described (S
Purification and Characterization of Isolated VHH Antibodies
The periplasmic expression and protein purification of recombinant FLAG-His6-tagged VHH was performed as described (C
A DNA construct was cloned to generate the bivalent proteins VHH1-LH-VHH2 tailed by Flag-tag and 6×HIS tag. “LH” stands for “long hinge” and is the structural upper hinge of the llama IgG2, AHHSEDPSSKAPKAPMA SEQ ID NO. 15 (Vu et al. 1997). The N-terminal antibody fragment was cloned in frame with the pelB signal sequence for potential periplasmic localization. VHH proteins were expressed and purified using Ni-NTA resins as described previously (C
Table 2 presents the ELISA data of purified monovalent and bivalent antibodies. Antibody titers to NA were measured by ELISA using microplates coated with (0.1 ug/well) NA antigens and serial dilutions of antibody. Bound VHH antibodies were detected with HRP conjugated mouse anti-FLAG IgG (Rockland Immunochemicals). NA inhibition activity of monospecific and multivalent antibodies was measured using a Neuraminidase assay (BioAssay Systems).
Note: Shown is ELISA data of the original VHH 27-8 and three different humanized VHH h27-8, h27-8GL and h27-8GL/h27-8GL against three different neuraminidase targets. The first three VHH are monovalent, the last one is a bivalent VHH. Shown is the reactivity compared to control protein used as target (BSA).
In accordance with the present invention, a polypeptide library is diversified by overexpression of sea lamprey CDA1 and its variants.
The invention described herein is of a composition and method for diversifying polypeptide libraries in yeast. Although some embodiments have been discussed above, other implementations and applications are also within the scope of the following claims. Although the invention herein has been described with reference to particular embodiments, it is to be understood that these embodiments are merely illustrative of the principles and applications of the present invention. It is therefore to be understood that numerous modifications may be made to the illustrative embodiments and that other arrangements may be devised without departing from the spirit and scope of the present invention as defined by the following claims.
The invention further relates to the following numbered embodiments:
A system and method for diversifying a protein of interest comprising: a) a first DNA construct having a nucleic acid molecule encoding a protein of interest operably linked to a promoter; b) a second DNA construct having a nucleic acid molecule encoding a second polypeptide operably linked to a promoter; c) a host cell comprising said first and second constructs, diversification of said first construct being dependent upon the expression of the second construct effectuated by said host cell genetic background, and d) diversification of said first construct is also effectuated by said host cell genetic background and the presence of mutation-inducing base analog chemicals.
A system as in one of the “A” Embodiments, wherein said first polypeptide is selected from a group of proteins with measurable functional activity including but not limited to target binding and enzyme activity.
A system as in one of the “A” Embodiments, wherein said first polypeptide is selected from a group of immunoglobulin heavy chain or light chain variable regions or polypeptide scaffolds including, but not limited to Anticalins, fibronectin type III domain—Adnectins, Designed Ankyrin Repeat Protein or DARPins and Centyrins.
A system as in one of the “A” Embodiments, wherein said immunoglobulin heavy chain or light chain variable regions can be from any organism.
A system as in one of the “A” Embodiments, wherein said first DNA construct is operably linked to a motif for a DNA binding protein domain.
A system as in one of the “A” Embodiments, wherein said motif for a DNA binding protein domain is including, but not limited to estrogen response elements.
A system as in one of the “A” Embodiments, wherein said second DNA construct encodes lamprey Petromyzon marinus cytidine deaminase, PmCDA1 protein (Seq. 1, Uniprot # A5H718).
A system as in one of the “A” Embodiments, wherein said DNA-modifying protein is a variant or derivative of sea lamprey Petromyzon marinus cytidine deaminase 1.
A system as in one of the “A” Embodiments, wherein said Petromyzon marinus cytidine deaminase is fused with a DNA binding domain.
A system as in one of the “A” Embodiments, wherein said DNA binding domain includes, but is not limited to the DNA binding domain of estrogen receptor and Gal4 transcriptional factor.
A system as in one of the “A” Embodiments, wherein at least one of said promoters in step a) and b) is an inducible promoter selected from the group consisting of galactose-inducible promoters GAL1 and GAL10, temperature regulatable like heat-shock inducible promoter HSP70, and copper-inducible CUP1 promoters.
Embodiment A12. A system as in one of the “A” Embodiments, wherein said mutation-inducing chemical is selected from the group consisting of purine or pyrimidine base analogs.
A system as in one of the “A” Embodiments, wherein said base analogue is 6-N-hydroxylaminopurine (HAP).
A system as in one of the “A” Embodiments, wherein said host cell is a yeast cell.
A system as in one of the “A” Embodiments, wherein said yeast is diploid or polyploid yeast.
A system as in one of the “A” Embodiments, wherein said host genotype includes inactivation of the Uracil-DNA glycosylase encoding UNG1 gene.
A system as in one of the “A” Embodiments, wherein said host genotype includes inactivation of the HAM1 gene.
A method in one of the “A” Embodiments, wherein said host cell is grown in conditions to activate said inducible promoter.
The method in one of the “A” Embodiments, wherein said host cell is grown in the presence of a base analogue.
The method in one of the “A” Embodiments, wherein said a base analogue includes, but is not limited to 6-N-Hydroxylaminopurine.
A yeast cell comprising: (A) a recombinant DNA that constitutively or inducibly expresses a cytidine deaminase comprising sequence with about 90% sequence identity or more with a cytidine deaminase domain of (i) SEQ ID NO. 2 or SEQ ID NO. 4, or (ii) a chimera between the two starting with SEQ ID NO. 3 or SEQ ID NO. 4 sequence and having one transition to end in SEQ ID NO. 1 or SEQ ID NO. 2 sequence, or (iii) a chimera between the two starting with SEQ ID NO. 1 or SEQ ID NO. 2 sequence and having one transition to end in SEQ ID NO. 3 or SEQ ID NO. 4 sequence; and (B) a second recombinant DNA that constitutively or inducibly expresses a binding scaffold protein for presentation on the outer surface of the yeast, wherein the cytidine deaminase as expressed by the first recombinant DNA is effective to contribute to a mutagenic process for inducing mutations in the binding scaffold protein of the yeast cell. Per the “comprising” language, the beginning and end language does not imply that the recombinant DNA, or the expressed protein begins or ends at a particular location.
Embodiment B1a. A yeast cell comprising: (A) a recombinant DNA that constitutively or inducibly expresses a cytidine deaminase comprising sequence with about 90% sequence identity or more with SEQ ID NO. 2, SEQ ID NO. 4, or a chimera between the two starting with SEQ ID NO. 3 or SEQ ID NO. 4 sequence and having one transition to end in SEQ ID NO. 1 or SEQ ID NO. 2 sequence; and (B) a second recombinant DNA that constitutively or inducibly expresses a binding scaffold protein for presentation on the outer surface of the yeast, wherein the cytidine deaminase as expressed by the first recombinant DNA is effective to contribute to a mutagenic process for inducing mutations in the binding scaffold protein of the yeast cell. Per the “comprising” language.
A method of generating a binding activity comprising: (A) cultivating a culture of yeast cells that comprise: (a) a first recombinant DNA that constitutively or inducibly expresses a cytidine deaminase with about 90% sequence identity with a cytidine deaminase domain of (i) SEQ ID NO. 2 or SEQ ID NO. 4, or (ii) a chimera between the two starting with SEQ ID NO. 3 or SEQ ID NO. 4 sequence and having one transition to end in SEQ ID NO. 1 or SEQ ID NO. 2 sequence, or (iii) a chimera between the two starting with SEQ ID NO. 1 or SEQ ID NO. 2 sequence and having one transition to end in SEQ ID NO. 3 or SEQ ID NO. 4 sequence; and (b) a second recombinant DNA that constitutively or inducibly expresses a binding scaffold protein for presentation on the outer surface of the yeast, wherein the culture of yeast cells expresses a library of binding scaffold proteins, wherein the cytidine deaminase as expressed by the recombinant DNA is effective to contribute to a mutagenic process for inducing mutations in the expressed binding scaffold proteins from the yeast cell culture; such that the cytidine deaminase and the scaffold protein are expressed; (B) contacting the culture with a mutagen; and (C) selecting a subset of yeast cells that bind to a given substance more strongly than the majority of the yeast cells.
A method of generating a binding activity comprising: (A) cultivating a culture of yeast cells that comprise: (a) a first recombinant DNA that constitutively or inducibly expresses a cytidine deaminase with about 90% sequence identity with SEQ ID NO. 2, SEQ ID NO. 4, or a chimera between the two starting with SEQ ID NO. 2 sequence and having one transition to end in SEQ ID NO. 1 sequence; and (b) a second recombinant DNA that constitutively or inducibly expresses a binding scaffold protein for presentation on the outer surface of the yeast, wherein the culture of yeast cells expresses a library of binding scaffold proteins, wherein the cytidine deaminase as expressed by the recombinant DNA is effective to contribute to a mutagenic process for inducing mutations in the expressed binding scaffold proteins from the yeast cell culture; such that the cytidine deaminase and the scaffold protein are expressed; (B) contacting the culture with a mutagen; and (C) selecting a subset of yeast cells that bind to a given substance more strongly than the majority of the yeast cells.
A yeast cell culture comprising: yeast cells comprising: (A) a recombinant DNA that constitutively or inducibly expresses a cytidine deaminase comprising sequence with about 90% sequence identity or more with a cytidine deaminase domain of (i) SEQ ID NO. 2 or SEQ ID NO. 4, or (ii) a chimera between the two starting with SEQ ID NO. 3 or SEQ ID NO. 4 sequence and having one transition to end in SEQ ID NO. 1 or SEQ ID NO. 2 sequence, or (iii) a chimera between the two starting with SEQ ID NO. 1 or SEQ ID NO. 2 sequence and having one transition to end in SEQ ID NO. 3 or SEQ ID NO. 4 sequence; and (B) a second recombinant DNA that constitutively or inducibly expresses a binding scaffold protein for presentation on the outer surface of the yeast, wherein the culture of yeast cells expresses a library of binding scaffold proteins, wherein the cytidine deaminase as expressed by the first recombinant DNA is effective to contribute to a mutagenic process for inducing mutations in the binding scaffold protein of the yeast cell.
A yeast cell culture comprising: yeast cells comprising: (A) a recombinant DNA that constitutively or inducibly expresses a cytidine deaminase comprising sequence with about 90% sequence identity or more with SEQ ID NO. 2, SEQ ID NO. 4, or a chimera between the two starting with SEQ ID NO. 3 or SEQ ID NO. 4 sequence and having one transition to end in SEQ ID NO. 1 or SEQ ID NO. 2 sequence; and (B) a second recombinant DNA that constitutively or inducibly expresses a binding scaffold protein for presentation on the outer surface of the yeast, wherein the culture of yeast cells expresses a library of binding scaffold proteins, wherein the cytidine deaminase as expressed by the first recombinant DNA is effective to contribute to a mutagenic process for inducing mutations in the binding scaffold protein of the yeast cell.
The yeast cell, method or cell culture of a “B” Embodiment, wherein the percent identity is about 95% or higher.
The yeast cell, method or cell culture of a “B” Embodiment, wherein the recited percent identity is to SEQ ID NO. 2.
The yeast cell, method or cell culture of a “B” Embodiment, wherein the cytidine deaminase comprises a fused to a DNA binding domain, and wherein the second recombinant DNA comprises the cognate DNA recognition sequence to which the binding domain binds, the recognition sequence vicinal to the DNA sequence encoding the binding scaffold protein.
The yeast cell, method or cell culture of a “B” Embodiment, wherein the DNA binding domain comprises the binding domain of estrogen receptor or GAL4 transcription factor.
The yeast cell, method or cell culture of a “B” Embodiment, wherein the binding scaffold protein is an immunoglobulin heavy chain variable region, a light chain variable region, combinations of light and heavy chain regions, Anticalins, fibronectin type III domain, Designed Ankyrin Repeat Protein or Centyrin.
The yeast cell, method or cell culture of a “B” Embodiment, wherein the first or second recombinant DNAs express the recited deaminase or binding scaffold protein utilizing a galactose-inducible promoter, a thermally inducible, or a copper-inducible promoter.
The yeast cell, method or cell culture of a “B” Embodiment, wherein the first or second recombinant DNAs express the recited deaminase or binding scaffold protein utilizing a galactose-inducible promoter GAL1, a galactose-inducible promoter GAL10, a heat-shock inducible promoter HSP70, or a copper-inducible CUP1 promoter.
The yeast cell, method or cell culture of a “B” Embodiment, wherein the yeast cell is diploid or polyploid.
The yeast cell, method or cell culture of a “B” Embodiment, wherein the yeast cell has a deleted or inactivated HAM1 gene.
The yeast cell, method or cell culture of a “B” Embodiment, wherein the yeast cell has a deleted or inactivated Uracil-DNA glycosylase encoding UNG1 gene.
The method of one of a “B” Embodiment, wherein the method further comprising inducing the expression of the cytidine deaminase or library.
The method of one of a “B” Embodiment, wherein the selecting comprising panning the cells over a surface having bound thereto the substance.
The method of one of a “B” Embodiment, wherein the selecting further comprising selecting by cell sorting cells that more strongly bind the substance linked to a color marker.
The method of one of a “B” Embodiment, wherein the mutagen is a nucleic acid base analog.
The method of one of a “B” Embodiment, wherein the mutagen is a purine or pyrimidine base analogs
The method of one of a “B” Embodiment, wherein the mutagen is 6-N-hydroxylaminopurine.
Publications and references, including but not limited to patents and patent applications, cited in this specification are herein incorporated by reference in their entirety in the entire portion cited as if each individual publication or reference were specifically and individually indicated to be incorporated by reference herein as being fully set forth. Any patent application to which this application claims priority is also incorporated by reference herein in the manner described above for publications and references.
All ranges recited herein include ranges therebetween, and can be inclusive or exclusive of the endpoints. Optional included ranges are from integer values therebetween (or inclusive of one original endpoint), at the order of magnitude recited or the next smaller order of magnitude. For example, if the lower range value is 0.2, optional included endpoints can be 0.3, 0.4, . . . 1.1, 1.2, and the like, as well as 1, 2, 3 and the like; if the higher range is 8, optional included endpoints can be 7, 6, and the like, as well as 7.9, 7.8, and the like. One-sided boundaries, such as 3 or more, similarly include consistent boundaries (or ranges) starting at integer values at the recited order of magnitude or one lower. For example, 3 or more includes 4 or more, or 3.1 or more. If there are two ranges mentioned, such as about 1 to 10 and about 2 to 5, those of skill will recognize that the implied ranges of 1 to 5 and 2 to 10 are within the invention.
This invention described herein is of a diversification system and methods of forming the same. Although some embodiments have been discussed above, other implementations and applications are also within the scope of the following claims. Although the invention herein has been described with reference to particular embodiments, it is to be understood that these embodiments are merely illustrative of the principles and applications of the present invention. It is therefore to be understood that numerous modifications may be made to the illustrative embodiments and that other arrangements may be devised without departing from the spirit and scope of the present invention as defined by the following claims.
Publications and references, including but not limited to patents and patent applications, cited in this specification are herein incorporated by reference in their entirety in the entire portion cited as if each individual publication or reference were specifically and individually indicated to be incorporated by reference herein as being fully set forth. Any patent application to which this application claims priority is also incorporated by reference herein in the manner described above for publications and references.
This application claims benefit of U.S. Provisional Patent Application No. 62/387,511 filed Dec. 24, 2015, which is incorporated herein by reference in its entirety.
Number | Date | Country | |
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62387511 | Dec 2015 | US |