Patent Grant
12297427
The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Nov. 30, 2016, is named 243734_000082_SL.TXT and is 76,261 bytes in size.
The invention is directed to methods for rapid cloning and expression of T-cell receptors (TCRs) and B-cell receptors (BCRs) and their use for drug screening, structural and functional studies and other applications. More particularly, the invention provides a method for rapid cloning of TCRs (e.g., paired αβ and γδ TCR chains) or BCRs (e.g., paired IgH or Igκ or Igλ) from single cells by CDR3 substitution using single cell PCR products and Gibson Assembly techniques and a pre-generated TCR (or BCR) library in an expression vector.
T cells play a vital role in the control of viral infections and tumors. T cells are activated by antigen presenting cells via interactions between peptide-major histocompatibility complex (pMHC) and TCRs. This interaction can induce proliferation and the development of effector functions, including cytokine production and cytotoxic activity. T cells can also infiltrate infected or transformed tissues, e.g. as tumor-infiltrating lymphocytes (TILs), to perform these effector functions1,2. However, in some chronic viral infections and tumors, responding effector T cells progressively get exhausted and become dysfunctional3,4,5. In addition, control of tumors and/or infection may require large numbers of highly reactive lymphocytes that cannot be achieved due to normal tolerance mechanisms. One effective method to overcome this barrier is the use of therapeutic adoptive transfer of lymphocytes2,6,7.
Adoptive transfer of lymphocytes such as in vitro expanded or TCR-engineered antigen specific T cells has been successfully used to control viruses and tumors in patients8,9,10,11,12. In vitro expansion of viral or tumor-specific T cells require significant time to prepare and the targets are not usually fully characterized. Lymphocytes expressing engineered TCRs and chimeric antigen receptors (CAR) target specific antigens, with CARs recognizing surface antigens through immunoglobulin-type interactions10,13 and TCRs recognizing tumor-associated pMHC complexes. CAR therapy directed against surface antigens requires a tumor-associated antigen that can be universally targeted (even on healthy, non-tumor tissue) without significant toxicity. Tumor-specific antigens that are targeted by TCRs represent an attractive alternative that can provide greater specificity and reduce non-tumor associated toxicities14,15,16. Additionally, engineered T cells expressing high-affinity antigen receptors can be conditioned to overcome immune tolerance, which has been a major limitation for immunotherapy14,15,17. Apart from the clinical applications, a robust system for the cloning and expression of TCRs is a valuable tool for the investigation of TCR structure and functions18,19,20.
Techniques to rapidly profile and clone antigen-specific TCRs have improved and shortened the process of TCR-engineered immunotherapy21,22. These approaches are useful contributions to the field and are able to handle large cell inputs very effectively. However, for certain applications, the reported methods still have some limitations. First, approaches that rely on deep sequencing and cloning of bulk sorted cells can still be limited by target cell numbers. In contrast, single cell approaches can utilize input sizes starting with a single cell but are less efficient at dealing with high cell number inputs (greater than 10,000 cells). As a result, single cell methods are best directed at defined samples such as antigen-specific responses or tissue-associated infiltrating cells. Second, for bulk sorting, pairing of TCR chains requires algorithmic imputation, which can have difficulty dealing with cells expressing two distinct TCR chains of one type (e.g. two TCRα chains), which are quite common. A recently reported algorithm has addressed this concern by pairing bulk processed TCRs using barcoded pools of cells 23. However, this method requires relatively large inputs to successfully pair and would likely not be appropriate for very small sample sizes as might be obtained from tissue biopsies or tetramer sorting of small populations.
Third, while currently reported methods are able to generate full length receptors either by synthesis or by 5′ RACE-associated approaches at the single cell level, these methods require expansion of the isolated cells prior to TCR isolation, which likely causes bias in the TCR repertoire in the subsequent analyses and/or can reduce efficiency. Lastly, the majority of antiviral and antitumor adoptive therapy has focused on αβ T cell clones due to their exquisite antigen specificity. However, γδ cells have also been shown to mediate antiviral and antitumor effects and are novel candidates for therapeutic development24,25.
To date, there is little research about profiling and utilizing the TCRγδ repertoire for therapeutic purposes. Applying γδ T cells for immunotherapeutic applications may be a promising future approach in conjunction with traditional TCRαβ techniques. Therefore, it is important to establish a system to define the repertoire and functional activity for γδ T cells. Additionally, improving efficiencies for cloning αβ TCRs from single cells may have complementary uses in the lab and in the clinic.
There is a great need in the art to develop a rapid, efficient and accurate cloning and expression method and/or system for specific TCRs, and uses thereof for screening TCR-mediated therapeutics, as well as for other research and/or clinical applications. The present invention fulfils such needs, and provides such methods and platforms.
In one aspect, the invention provides a method for cloning a T cell receptor (TCR) from a single T cell, wherein said method comprises:
In one embodiment, said T cell is a human or a mouse αβ or γδ T cell.
In one embodiment, the method comprises sorting of single T cells prior to step (a). In one specific embodiment, T cells are not stimulated prior to sorting.
In one embodiment, the primer mixture comprises sense primers comprising T-cell receptor gamma variable (TRGV) sequences and/or T cell receptor delta variable (TRDV) sequences and antisense primers comprising T-cell receptor gamma constant (TRGC) sequences and/or T-cell receptor delta constant (TRDC) sequences. In one specific embodiment, the primer mixture comprises 9 TRGV and 8 TRDV sense primers and single TRGC and TRDC antisense primers. In another specific embodiment, the primer mixture comprises 5 external and 5 internal TRGV and 13 external and 13 internal TRDV sense primers and single TRGC and TRDC antisense primers. In one embodiment, the TRGV and/or TRDV sense primers and the TRGC and/or TRDC antisense primers are selected from the primers listed in Table 1. In one embodiment, the TRGV and/or TRDV sense primers and the TRGC and/or TRDC antisense primers are selected from the primers listed in Table 6.
In one embodiment, the single cell RT-PCR of γδ or αβ TCR and sequencing are performed within not more than 2 days.
In one embodiment, the method further comprises cloning the resulting αβ or γδ TCR CDR3 DNA sequences into the TCRαβ and/or TCRγδ library constructed using the method described below.
In a related aspect, the invention provides a method for constructing a TCRαβ and/or TCRγδ library in an expression vector, comprising:
In one embodiment of the above library construction method, the expression vector is a retroviral or lentiviral expression vector. In one embodiment, the ligation in step (b) is performed using Gibson Assembly Cloning techniques. In one specific embodiment, Gibson Assembly Cloning techniques are optimized to clone synthesized TRGV/TRAV and TRDV/TRBV DNA fragments using g-blocks or other synthesized DNA fragments (e.g., long primers that are then annealed). In one embodiment, the TCRαβ and/or TCRγδ library is constructed after a single-cell amplification and synthesized paired TRGV/TRDV or TRAV/TRBV receptors based on the sequence data. In one embodiment, the TCRαβ and/or TCRγδ library is constructed in 5 to 10 days. In one embodiment, the TCRαβ and/or TCRγδ library is used for drug screening or identification of TCRαβ- and/or TCRγδ-specific ligands.
In one embodiment of the above library construction, the method comprises substituting CDR3 regions of the existing clones in the TCRαβ and/or TCRγδ library with (i) products of RT-PCR performed using a primer mixture on a single T cell to obtain paired αβ or γδ TCR CDR3 DNA sequences comprising a partial variable (V) region, CDR3 region, and a partial constant (C) region and (ii) a linker DNA for overlap extension of PCR cloning. In one specific embodiment, said T cell is a human or a mouse αβ or γδ T cell. In one specific embodiment, the method comprises sorting of single T cells prior to RT-PCR. In one specific embodiment, T cells are not stimulated prior to sorting. In one specific embodiment, the primer mixture comprises sense primers comprising T-cell receptor gamma variable (TRGV) and/or T cell receptor delta variable (TRDV) and antisense primers comprising T-cell receptor gamma constant (TRGC) and/or T-cell receptor delta constant (TRDC) sequences. In one specific embodiment, the primer mixture comprises 9 TRGV and 8 TRDV sense primers and single TRGC and TRDC antisense primers. In one specific embodiment, the primer mixture comprises 5 external and 5 internal TRGV and 13 external and 13 internal TRDV sense primers and single TRGC and TRDC antisense primers. In one specific embodiment, the TRGV and/or TRDV sense primers and the TRGC and/or TRDC antisense primers are selected from the primers listed in Table 1. In one specific embodiment, the TRGV and/or TRDV sense primers and the TRGC and/or TRDC antisense primers are selected from the primers listed in Table 6. In one specific embodiment, said linkers are overlapping with the non-variant sequences of the TCRα/γ and TCRβ/δ single cell RT-PCR products. In one specific embodiment, said linker sequences are selected from those listed in Table 3. In one specific embodiment, the resulting TCRαβ and/or TCRγδ chains with CDR3 substitutions are used for T cell-mediated immunotherapy.
In a related aspect, the invention provides a TCRαβ and/or TCRγδ library constructed using any of the above methods. In another related aspect, the invention provides a host cell (e.g., a Nur-77-GFP Jurkat 76 cell or a Nur-77-Luciferase Jurkat 76 cell) comprising said TCRαβ and/or TCRγδ library construct.
In another aspect, the invention provides a method for cloning a B cell receptor (BCR) from a single B cell, wherein said method comprises:
In one embodiment, said B cell is a human or a mouse B cell. In one embodiment, the method comprises sorting of single B cells prior to step (a).
These and other aspects of the present invention will be apparent to those of ordinary skill in the art in the following description, claims and drawings.
In
In
The present invention provides a rapid, efficient and accurate cloning and expression method and system for specific TCRs (e.g., paired αβ and γδ TCR chains from single cells) which can be used for drug screening (e.g., for T cell-mediated anti-tumor or anti-infective immunotherapy), for structuring and functional analysis of TCRs, and other applications. The invention addresses the non-specific, labor-intensive and time-consuming issues of prior PCR-based cloning methods and provides a high-throughput, accurate and efficient method of TCR engineering for therapeutic and research applications.
In conjunction with single cell multiplex PCR techniques for TCRαβ or TCRγδ profiling26,27, and Gibson Assembly® cloning of synthesized DNA, the invention provides rapid sequencing and cloning of specific TCRs in an expression vector (e.g., retroviral expression vector). By generating TCR libraries, the invention provides a cloning and expression method and system that is significantly accelerated by only requiring the substitution of the CDR3 region, resulting in TCR clones in appropriate expression vectors in as little as five days after cell isolation. The invention provides highly robust, inexpensive, efficient, and high-throughput means for TCR engineering for therapeutic and research applications.
In certain embodiments, the invention provides a method of single-cell amplification of paired TCR CDR3 α/γ and CDR3 β/δ regions comprising the steps of (a) sorting of single human αβ or γδ T cells; (b) performing RT-PCR to obtain a single-cell cDNA; and (c) amplifying the single-cell cDNA obtained in step (b) in a second round PCR with a primer mixture of TRGV and TRDV sense primers and TRGC and TRDC antisense primers. In one embodiment, the single-cell cDNAs are amplified with a primer mixture comprising nine (9) T-cell receptor gamma variable (TRGV) and/or eight (8) T-cell receptor delta variable (TRDV) sense primers and a single T-cell receptor gamma constant (TRGC) and/or T-cell receptor delta constant (TRDC) antisense primer. Non-limiting examples of external and internal sense primers targeting TRGV and TRDV and antisense TRGC and TRDC primers are listed in Table 1, below. Specific non-limiting examples of a method for sorting single cells, as well as conditions for RT-PCR and nested PCRs, are provided below (see Example 1, Materials & Methods).
In certain embodiments, the invention also provides a method of production of TCRαβ and TCRγδ library in an expression vector, comprising the steps of (a) synthesizing multiple pairs of TRGV and TRDV DNA fragments with a 15-20 bp overlap in the sequence in the 2A region based on the TRGV/TRDV usage in human apheresis ring samples, and (b) performing a three-way ligation with a linearized expression vector (e.g., a retroviral vector, which is convenient for the future applications, like transduction of cell lines and TCR-transgenic mice) using Gibson Assembly® Cloning or another type of ligation, including, e.g., conventional T4-mediated ligation. In certain embodiments, the TCRαβ and/or TCRγδ library is human library comprising the human TCRαβ and TCRγδ. In certain embodiments, the production of TCRαβ and TCRγδ library is performed after the single-cell amplification and paired TRGV/TRDV usage based on the sequence data. Exemplary primers targeting the 2A regions of human CD3δ, γ, ϵ and genes are provided in Tables 2A & 2B.
The Gibson Assembly kit is an enzyme and buffer mix designed to optimize the overlap ligation of g-block gene fragments. In certain embodiments, Gibson Assembly protocol is optimized to synthesize the TRGV and TRDV DNA fragments or genes using g-block technique, IDT DNA). However, the ligation reaction can be performed using other suitable ligases known and available in the art. Using the methods of the present invention, a TCR library can be constructed in as fast as 10 days. As long as the library is established, it can be applied to substitute CDR3 regions from a new patient sample, which can dramatically reduce the cloning time from 10 days to 5 days. This could be beneficial for both adoptive transfer therapy and personalized therapy.
The invention provides a rapid cloning method based on the TCR library constructed, e.g., the TCRαβ and TCRγδ library, comprising the step of generating full-length paired αβ or γδ TCR chains by CDR3 substitution using multiplex PCR products and a linker DNA (overlap extension PCR). In certain embodiments, the linkers contribute to simultaneously substitute CDR3 regions of both TCRα/γ and TCRβ/δ. The linkers are overlapping with the single cell PCR products, therefore, no additional PCR steps are needed. In certain embodiments, the TCRα/γ and TCRβ/δ single cell PCR products and the linkers are mixed together and an overlap PCRs are performed, and then the PCR products generated from the overlap PCRs are used to substitute the CDR3 regions in the cloning library. Exemplary human TCRγδ linker sequences are provided in Table 3, below.
The methods of the present inventions improve the speed and specificity for cloning paired TCRs. With single cell analyses, the cloned paired TCRs of the present invention are more “specific” than examining T cell receptors in bulk because both chains of the receptor are from the same cell. The invention allows rapid cloning of TCRs that are responding to an infection or a tumor, which could be useful in developing targeted cell therapies, e.g., by reintroducing those receptors into the patient's cells to assist in mounting a more effective response. The TCR sequences themselves can also be useful for understanding what targets the response is against. Although there is no simple way of decoding the target from the TCR sequence, databases and/or computer algorithms can be developed to evaluate the relationship on the antigens and the elicited T-cell responses via various TCRs. Furthermore, the invention provides an efficient and accurate TCR expression system for TCRs in a reporter cell line, which can be used for screening specific antigens directly. TCR sequencing can also be used for the detection of minimal residual disease in leukemia and lymphoma. Many tumors have rearranged their TCRs. In these cases, the specific TCR sequence in the tumor becomes a lineage “barcode” for the tumor itself. The methods of the invention can provide TCR sequencing information to determine the presence and/or quantity of tumor cells.
In describing the present invention, the following terms will be employed, and are intended to be defined as indicated below.
“CDR3 region” or “the third complementarity determining region” is defined herein as the region from codon positions 105 to the end of the V-REGION in germline gDNA or cDNA, codon positions 105 to 117 in V-DOMAIN of rearranged gDNA or in cDNA (all the position numbers are according to the IMGT unique numbering; see Lefranc, M.-P., The Immunologist, 7, 132-136 (1999) and www.imgt.org/IMGTScientificChart/Nomenclature/IMGT-FRCDRdefinition.html).
As used herein the term “partial variable region” or “partial V region” is determined by the position of the internal forward primers targeting the amplified V-region of interest (e.g., a, β, γ, δ; see, e.g., Tables 8-11) until the codon position 105 (all the position numbers are according to the IMGT unique numbering; see Lefranc, M.-P., The Immunologist, 7, 132-136 (1999) and www.imgt.org/IMGTScientificChart/Nomenclature/IMGT-FRCDRdefinition.html).
As used herein the term “partial constant region” or “partial C region” refers to a region that includes the first codon of the C region until a position defined by the reverse internal primer used to amplify the C region of interest (e.g., α, β, γ, δ; see Tables 8-11).
The term “corresponding TCR library” means the same variable (V) family usage.
It must be noted that, as used in this specification and the appended claims, the singular forms “a,” “an” and “the” include plural referents unless the content clearly dictates otherwise.
The terms “subject,” “individual,” and “patient,” are used interchangeably herein and refer to any mammalian subject for whom diagnosis, prognosis, treatment, or therapy is desired, particularly humans. Other subjects may include cattle, dogs, cats, guinea pigs, rabbits, rats, mice, horses, and so on. In some cases, the methods of the invention find use in experimental animals, in veterinary application, and in the development of animal models for disease, including, but not limited to, rodents including mice, rats, and hamsters; primates, and transgenic animals.
The term “about” means within an acceptable error range for the particular value as determined by one of ordinary skill in the art, which will depend in part on how the value is measured or determined, i.e., the limitations of the measurement system. For example, “about” can mean within an acceptable standard deviation, per the practice in the art. Alternatively, “about” can mean a range of up to ±20%, preferably up to ±10%, more preferably up to ±5%, and more preferably still up to ±1% of a given value. Alternatively, particularly with respect to biological systems or processes, the term can mean within an order of magnitude, preferably within 2-fold, of a value. Where particular values are described in the application and claims, unless otherwise stated, the term “about” is implicit and in this context means within an acceptable error range for the particular value.
In accordance with the present invention there may be employed conventional molecular biology, microbiology, and recombinant DNA techniques within the skill of the art. Such techniques are explained fully in the literature. See, e.g., Sambrook, Fritsch & Maniatis, Molecular Cloning: A Laboratory Manual, Second Edition (1989) Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (herein “Sambrook et al., 1989”); DNA Cloning: A practical Approach, Volumes I and II (D. N. Glover ed. 1985); Oligonucleotide Synthesis (M J. Gait ed. 1984); Nucleic Acid Hybridization (B. D. Hames & S. J. Higgins eds. (1985»; Transcription and Translation (B. D. Hames & S. J. Higgins, eds. (1984»; Animal Cell Culture (R. I. Freshney, ed. (1986»; Immobilized Cells and Enzymes (IRL Press, (1986»; B. Perbal, A practical Guide To Molecular Cloning (1984); F. M. Ausubel et al. (eds.), Current Protocols in Molecular Biology, John Wiley & Sons, Inc. (1994); among others.
The present invention provides several useful techniques for the analysis of TCR biology, including a single cell based protocol for γδ TCR amplification, a rapid protocol for TCR cloning and expression, and a novel platform for functional characterization of TCR clones (see
The most prominent recent immunotherapy approaches involve T cell checkpoint blockade inhibitors51. However, these therapies depend on the presence of significant numbers of anti-tumor T cell responses. The ex vivo expansion of tumor infiltrating lymphocytes has also been successful, but is time consuming52. The method of the present invention significantly accelerates the amount of time needed to generate large numbers of anti-tumor T cells, by allowing the efficient transduction of identified anti-tumor receptors. The key to the application of the invention of directed T cell immunotherapy is the rapid and accurate isolation and cloning of paired TCRs. Thus far, various methods have been developed for the cloning of TCR genes by traditional PCR, but the acquisition and expression of TCRs is often labor-intensive, time-consuming, expensive, and non-specific. The present invention provides efficient acquisition of TCR gene products for cloning based on single cell isolation, with an amplification success rate of isolated paired single cell TCRγ and TCRδ CDR3 products of 71.25±18.75% based on total sorted single cells in each sample.
The invention also provides a platform for screening TCR activation after cloning. By inserting the Nur77 reporter into a Jurkat 76 TCRα-β-cell line, a useful system for monitoring specific TCR activation was generated, as demonstrated by stimulation of PB1-NJ76 by its cognate influenza-derived peptide and stimulation of TRGV9/TRDV2 T cells with, e.g., zoledronic acid.
In certain embodiments, the invention employs the insertion of Nur77-GFP BAC DNA into the Jurkat cell line as a reporter cell line. Prior approaches to detect T cell activation include CD69 expression on the cell surface22, and detection of IFNγ, IL-2, and TNFα protein levels in cell culture supernatants by ELISA21,22. These conventional methods have some shortcomings. For instance, CD69 is common activation marker of T cells, so it cannot show the specific activation of T cells through TCR signaling-bystander activation can occur. Detection of IFNγ, IL-2 and TNFα by ELISA is time-consuming (2 days) and expensive, and Detection of IFNγ, IL-2 and TNFα by real-time is labor-intensive (requires RNA isolation), time-consuming (at least a day).
The Nur77-GFP system has been demonstrated to reflect specific TCR triggering after stimulation40,41,42, instead of activation by other receptors on the cell surface, like TLRs, NKG2A/2D, or other inhibitory receptors. Furthermore, GFP is directly assayable by flow cytometry without any secondary processing. The Nur77-GFP system allows rapid and accurate detection of specific T cell stimulation in a high-throughput manner. In certain embodiments, the invention provides that zoledronic acid induces the GFP expression of TRGV9/TRDV2 Nur77-GFP cells, demonstrating that the invention platform is functional, and zoledronic acid can be used in combination with TRGV9/TRDV2-expressing cells as a positive control for the test platform and that peptides can be used in combination with their cognate TRBV/TRAV-expressing cells (as demonstrated in
Therefore, the present invention provides a novel platform and/or system that can be used to test different molecules directly by stimulating the Nur77-GFP Jurkat cell line, and characterizing and quantifying the stimulation based on GFP expression by flow cytometry. The platform of the present invention is faster, easier and more inexpensive (no need to stain) to perform, and can be used to screen TCR-activating or modifying drugs in a high-throughput screening manner as compared to prior art platforms.
In other embodiments, a Nur77-Luciferase reporter, which has a lower signal to noise ratio, is included in the Nur77-GFP Jurkat cell line to decrease the background for certain types of drug screening. Insertion of Nur77-Luciferase BAC DNA into the Jurkat cell line instead of Nur77-GFP can be undertaken, followed by luciferase detection in various assays that include high-throughput screening platforms. The luciferase detection may be conducted with between 5×104 to 2.5×105 cells per well, or about 1×105 cells per well, for highly sensitive detection.
Another application of the Nur77-GFP system is to screen for compounds that inhibit T cell activation. The Nur77-GFP system of the invention can be used for drug screening, clinical applications, and basic immunology research.
Considering the variability of CDR3 sequences and TCR variable regions (approximately 1018 combinations in human TCRγδ cells and 1016 combinations for TCRαβ cells53) and the complexity of cloning all the different clones de novo, the invention provides a method using overlap extension PCR of a linker molecule with amplified single cell CDR3 products and a constructed γδ (or αβ) TCR library to rapidly (less than 5 days) generate diverse TCR clones. Setting up a TCR clone library with all possible combination of TCRγ/TCRδ or TCRγ/TCRα pairings and a DNA linker library allows the achievement of superior speed by overcoming the need to synthesize the hypervariable CDR3 portion of the DNA. In the method of the present invention, as soon as the sequence information of the TCR CDR3 region from the single-cell PCR and their family usage are known, the relevant clone can be picked up from the library with the required TRBV and TRAV families to use as a backbone for the final construct. The single-cell PCR products of TCRβ/γ and TCRα/δ can then be linked together by using two terminal primers and a DNA linker by overlapping PCR. Next, this target gene can be substituted directly into the existing clones and the irrelevant CDR3s can be replaced with the specific ones while preserving the family usage. In certain embodiments, new CDR3s of TRGV9-TRDV2 are put into the existing cloning of TRGV9-TRDV2 vector with different CDR3s by overlapping extension PCR. With the method of the present invention, cloning TCR genes can be achieved within 5 days.
As compared to prior art methods21,22, important advantages of the methods of the present invention are as follows:
The rapid TCR cloning method of the present invention is very useful for immunotherapy. Tumor-specific T cells have been characterized by broad non-specific surface phenotypes that can be used to isolate, clone, and express potential tumor-targeted clones54. The recent advancement of tumor sequencing has allowed for identification of tumor neoantigens and overexpressed self-antigens55,56,57,58. Combining these technologies will allow characterizion and tailoring of anti-tumor therapy.
T cell transfers have also been used for the treatment of opportunistic infections in immunosuppressed patients, particularly after hematopoietic stem cell transplant. The reactivation of herpes viruses like human cytomegalovirus and Epstein-Barr virus is a clinical dilemma that cannot always be addressed with antivirals24,59,60. Analogous to TIL therapies, ex vivo expansion of antiviral T cell specificities can be clinically useful, but suffers from similar workflow limitations. By generating a library of specific TCR constructs reactive against a range of viruses and HLA types, TCR-directed therapies could be used prophylactically or immediately at the earliest signs of reactivation.
In addition to these therapeutic applications, the method of the present invention significantly improves the workflow for cloning and expressing TCRs for study in vitro. This can include the characterization of biochemical features of the TCR-peptide-MHC interaction, or, in the case where ligands have not been identified transduced cell lines can be used for the screening of novel antigens. This is particularly useful in the context of γδ T cells, where very few ligands have been identified and confirmed18,61. The GFP reporter line engineered can be used directly in high-throughput screening platforms; alternative reporters (such as, e.g., luciferase) can be easily substituted as well.
The present invention is also described and demonstrated by way of the following examples. However, the use of these and other examples anywhere in the specification is illustrative only and in no way limits the scope and meaning of the invention or of any exemplified term. Likewise, the invention is not limited to any particular preferred embodiments described here. Indeed, many modifications and variations of the invention may be apparent to those skilled in the art upon reading this specification, and such variations can be made without departing from the invention in spirit or in scope. The invention is therefore to be limited only by the terms of the appended claims along with the full scope of equivalents to which those claims are entitled.
Subjects and peripheral blood mononuclear cell (PBMC) samples. Samples were obtained using research protocols approved by St. Jude Children's Research Hospital's institutional review boards (IRB) (Memphis, Tenn.). Peripheral whole blood was collected from heparinized apheresis rings from healthy immunocompetent individuals not taking immunomodulatory pharmaceutical agents. PBMCs were isolated via density gradient centrifugation (GE Healthcare Ficoll-Paque PLUS), and red blood cells (RBCs) were removed using RBC lysis buffer (8.3 g NH4Cl, 1 g KHCO3, and 1 ml 0.1% Phenol Red in 1 L distilled water). Isolated PBMCs were frozen in −80° C. for future use. All PBMCs used in the paper were stored frozen. Compared to fresh PBMC data from healthy apheresis rings, frozen PBMCs did not have a significantly lower success rate for single-cell amplification.
Single cell sorting and staining. PBMCs were treated with human FcR blocking reagent (Miltenyi Biotec) on ice for 20 minutes. Human TCRγδ cells were isolated by staining with PE-conjugated anti-human TCRγ/δ (Biolegend, clone: B1), FITC-conjugated anti-human CD3 (Biolegend, clone: OKT3), a dump gate consisting of APC-conjugated anti-human CD11b/CD14/CD19 (Biolegend, CD11b clone: ICRF44; Biolegend, CD14 clone: HCD14; Biolegend, CD19 clone: HIB19) and Live/Dead Violet exclusion dye (Invitrogen, L34955) on ice for 30 minutes. After staining, TCRγ/δ+ CD3+ cells were sorted directly into a 96-well PCR plate (Biorad) with a sorter (Model sy3200, Sony Biotech Synergy sorter) by the following gating strategy: autofluorescence gate−lymphocytes gate−single cell gate−live/dead gate−dump gate (CD11b/14/19)−TCRγδ/CD3 gate (
Reverse transcription, multiplex, nested single cell PCR, and sequencing. cDNA from TCRγδ and TCRαβ mRNA was reverse transcribed directly from the sorted and stored single cells in the PCR plate without any RNA extraction step using the iScript cDNA Synthesis Kit (Bio-Rad) in a 2.5 μl reaction mix as per the method described previously26. The cDNA synthesis was carried out by incubating at 25° C. for 5 min, 42° C. for 30 min, and 80° C. for 5 min (For the first round and second round of PCR). Alternatively, the SuperScript® VILO cDNA synthesis kit was used which produces a higher success rate for single cell PCR by incubating the reaction mixture at 25° C. for 10 min, 42° C. for 60 min, and 80° C. for 5 min. The TCRαβ transcripts from each cell were amplified by a multiplex nested PCR strategy as described previously26,27. For amplification of TCRγδ transcripts, the overall strategy was similar to the published TCRαβ amplification (95° C. for 2 min, followed by 35 cycles of 95° C. for 20 s, 53° C. for 20 s, and 72° C. for 45 s, followed by final extension of 72° C. for 7 min.), except for the primers described in Table 1.
Nine (9) TRGV external sense primers, nine (9) TRGV internal sense primers, eight (8) TRDV external sense primers and eight (8) TRDV internal sense primers targeted for individual TRGV and TRDV families were designed based on the sequences derived from the IMGT database62. For the antisense primer, single TRGC external, TRGC internal, TRDC external, and TRDC internal primers complementary to the published TRGC and TRDC sequences in IMGT were designed. Human TRAV14/DV4, TRAV23/DV6, TRAV29/DV5, TRAV36/DV7, and TRAV38-2/DV8 are shared primers in TRAV and TRDV primer sets.
The primers were synthesized by IDT and stored at −20° C. at a stock concentration of 100 μM in TE with low EDTA (pH8.0). The primers for each category (sense external, sense internal of TRGV and TRDV) were combined so that the final concentration of each primer in the mixture was 10 μM. The antisense primers were diluted to 10 μM. The PCR conditions for the TCRγδ nested PCR were 95° C. for 2 min, followed by 35 cycles of 95° C. for 20 s, 53° C. for 20 s, and 72° C. for 45 s, followed by final extension of 72° C. for 7 min. The PCR products were run on a 2% agarose gel to check for the success rate of the PCR as well as contamination following which the products were purified by a modified Exonuclease I—rShrimp alkaline phosphatase (ExoSAP-IT®) method63 to eliminate unincorporated primers and dNTPs for high quality DNA sequencing. 1 μl of the single cell PCR product was added into the mixture of 4.6 μl of Tris-Cl (50 mM, pH8.0), 0.2 μl of Exonuclease I and 0.2 μl of rShimp alkaline phosphatase and was incubated at 37° C. for 15 min and 80° C. for 15 min. The purified PCR products were sequenced using the relevant TRAC, TRBC, TRGC or TRDC primer. A schematic of the PCR strategy is shown in
gBlock® gene fragments, Gibson Assembly® and Transformation. The gBlock® gene fragments encoding the library of TRGVs and TRDVs were obtained from Integrated DNA Technologies (IDT). The expression vector pMICherry (10 μg), which was modified from the parental pMIGII64 by changing GFP to an mCherry reporter, was double digested by EcoR I (20 units) and Xho I (20 units) restriction enzymes (New England Biolabs) at 37° C. for 3 h as per manufacturer's instruction. Agarose gel purified-linearized pMICherry vector (100 ng) and 2×TCR gBlock inserts were ligated in a three-way ligation, including the TCRγ gene, TCR gene, and linearized vector by using the Gibson Assembly® Cloning kit (New England Biolabs) per manufacturer's instructions. Two microliters of the ligation mixture was transformed into DH5α Competent E. coli (New England Biolabs) per manufacturer's instructions.
Generation of human CD3 constructs. Human CD3 δ, γ, ϵ and δ genes were amplified from human PBMC cDNA using the primers in Table 2a. All the genes were linked together by overlap PCR with species-specific 2A regions inserted35. The types and amino acid sequences of the 2As used are shown in Table 2b. The CD3 gene complex was then cloned into an MSCV-based retroviral vector that contains an IRES31,32,65 and ametrine as a reporter gene.
asigna virus)
DNA Isolation, Cell Culture and Transfection. Recombinant pMICherry plasmids with full length TCRαβ or TCRγδ inserts were isolated in small scale by using a NucleoSpin® Plasmid kit (Clontech) and in large scale for transfection using a Plasmid Midi kit (Qiagen) per the manufacturer's instructions. The Neon® Transfection System was used to transfect 10 μg TCRαβ or γδ DNA in the pMICherry vector into the human Jurkat 76 TCRα−β− cell line (2×107 cells/mL, 100 μl)66, followed by three pulses with a voltage of 1,350V and a width of 10 ms. The transfected cells were cultured for 48 h before being assayed for TCRαβ or TCRγδ expression on the surface by FACS analysis. The human Jurkat 76 cells TCRα−β− cell line was cultured in complete-RPMI 1640 medium, which is RPMI 1640 with 10% of fetal bovine serum, 1% Penicillin Streptomycin, and 1% L-glutamine at 37° C. and 5% CO2.
Immunofluorescent and flow cytometric analysis For surface staining, cells (1-5×105) were harvested from culture and washed with FACS buffer (PBS with 1% of BSA and 0.1% sodium azide) prior to staining. The cells were treated with human FcR blocking reagent (Miltenyi Biotec) on ice for 20 min, and cells were then treated with various fluorescent conjugated antibodies against cell surface markers in FACS buffer. Human γδ T cells were stained with APC-conjugated anti-human TCRγ/δ (Biolegend, clone: B1) or APC-conjugated anti-human TCRα/β (Biolegend, clone: IP26) and Pacific Blue-conjugated anti-human CD3 (Biolegend, clone: OKT3). For influenza-specific tetramer staining, cells (1-5×105) were stained with APC-conjugated Influenza-M1 tetramer (Beckman Coulter, HLA-A*0201, GILGFVFTL (SEQ ID NO: 146)) in FACS buffer at room temperature for 1 h prior to surface staining with the same staining antibodies described.
Modification of the CDR3 region by two-step overlap extension PCR cloning The substitution of the CDR3 was carried out by an overlap extension PCR cloning protocol28. A schematic diagram of the procedure is shown in
bold: 2A sequence; italic: TRDVx sequence
AAAGCAAGCAGGAGACGTGGAAGAAAACCCCGGTCCCA
GCAAGCAGGAGACGTGGAAGAAAACCCCGGTCCC
ATGC
AGAGGATCTCCTCCCTCATCCATCTCTCTCTCTTCTGG
GCAGGAGTCATGTCAGCCATTGAGTTGGTGCCTGAACA
CCAAACAGTGCCTGTGTCAATAGGGGTCCCTGCCACCC
TCAGGTGCTCCATGAAAGGAGAAGCGATCGGTAACTAC
TATATCAACTGGTACAGGAAGACCCAAGG3′
AAAGCAAGCAGGAGACGTGGAAGAAAACCCCGGTCCC
A
TGATTCTTACTGTGGGCTTTAGCTTTTTGTTTTTCTAC
AGGGGCACGCTGTGTGACAAAGTAACCCAGAGTTCCCC
GGACCAGACGGTGGCGAGTGGCAGTGAGGTGGTACTGC
TCTGCACTTACGACACTG3′ (SEQ ID NO: 52)
AAAGCAAGCAGGAGACGTGGAAGAAAACCCCGGTCCC
A
TGTCACTTTCTAGCCTGCTGAAGGTGGTCACAGCTTCA
CTGTGGCTAGGACCTGGCATTGCCCAGAAGATAACTCA
AACCCAACCAGGAATGTTCGTGCAGGAAAAGGAGGCTG
TGACTCTGG3′ (SEQ ID NO: 53)
AAAGCAAGCAGGAGACGTGGAAGAAAACCCCGGTCCC
A
TGGCCATGCTCCTGGGGGCATCAGTGCTGATTCTGTGG
CTTCAGCCAGACTGGGTAAACAGTCAACAGAAGAATGA
TGACCAGCAAGTTAAGCAAAATTCACCATCCCTGAGCG
TCCAGGAAGGAAGAATTTCTATTCTGAACTGTGACTAT
ACTAACAGCATGTTTGATTATTTCCTATGGTACAAAAA
ATACCCTGCTGAAGGTCCTACATTCCTGATATC3′
AAAGCAAGCAGGAGACGTGGAAGAAAACCCCGGTCCC
A
TGGACAAGATCTTAGGAGCATCATTTTTAGTTCTGTGG
CTTCAACTATGCTGGGTGAGTGGCCAACAGAAGGAGAA
AAGTGACCAGCAGCAGGTGAAACAAAGTCCTCAATCTT
TGATAGTCCAGAAAGGAGGGATTTCAATTATAAACTGT
GCTTATGAGAACACTGCGTTTGACTACTTTCCATGGTA
CC3′ (SEQ ID NO: 55)
AAAGCAAGCAGGAGACGTGGAAGAAAACCCCGGTCCC
A
TGATGAAGTGTCCACAGGCTTTACTAGCTATCTTTTGG
CTTCTACTGAGCTGGGTGAGCAGTGAAGACAAGGTGGT
ACAAAGCCCTCTATCTCTGGTTGTCCACGAGGGAG3′
GCAAGCAGGAGACGTGGAAGAAAACCCCGGTCCC
ATGG
CATGCCCTGGCTTCCTGTGGGCACTTGTGATCTCCACC
TGTCTTGAATTTAGCATGGCTCAGACAGTCACTCAGTC
TCAACCAGAGATGTCTGTGCAGGAGGCAGAGACCGTGA
CCCTGAGCTGCACATATGACACCAGTGAGAGTGATTAT
TATTTATTCTGGTACAAGCAGCCTCCCAG3′
Nur77-GFP Jurkat 76 TCRα−β− cell line. To characterize the functionality of TCRαβ or γδ clones, we established the Nur77-GFP Jurkat 76 TCRα−β− cell line (NJ76 cells). After linearization of a Nur77-GFP BAC clone (constructed based on pTARBAC)40 by mixing 10 μg BAC DNA, 2 μl 10× reaction buffer, 10 units of PI-SceI restriction enzyme (New England Biolabs), and nuclease-free water to make the volume up to 20 μl with incubation at 37° C. for 3 h and inactivation at 65° C. for 20 min, 80 μl of nuclease-free water, 15 μl of sterile sodium acetate (3M, pH7.0), and 300 μl of ethanol were added to the reaction mixture, which was then centrifuged at 12,000 g for 30 min at 4° C. The resulting DNA pellet was washed with 75% ethanol, dried in the air, and resuspended by Tris-EDTA buffer (pH 8.0). The Neon® Transfection System following the manufacturer's instruction was used to transfect the linearized BAC DNA into the human Jurkat 76 TCRα−β− cell line (2×107 cells/mL, 100 ul), and pulsed three times with a voltage of 1,350V and a width of 10 ms. Cells were then cultured in complete-RPMI 1640 medium containing 500 ug/ml Geneticin (Invitrogen) for selection.
Stimulation of KbPB1703+TCRαβ+ NJ76 cells (PB1-NJ76) by flu peptide PB1. NJ76 cell transfected with a murine KbPB1703-specific TCRαβ derived from influenza-infected mice and transfected cells were incubated with mouse splenocytes (cell number ratio of PB1-NJ76/splenocytes is 2:1), the influenza PB1703-711 peptide (1 μM/ml), mouse splenocytes and peptide, and mouse α-CD3 (2C11; 10 μg/ml) and human α-CD28 (CD28.2; 10 μg/ml) in c-RPMI 1640 medium at 37° C. for 4 h. The GFP expression in the mouse TCRαβ+CD3+ cell population was quantified by flow cytometry.
Stimulation of TRGV9/TRDV2-NJ76 cells by Zoledronic acid. NJ76 cells transfected with a TRGV9/TRDV2 clone were incubated with 50 μg/ml zoledronic acid (Zometa, Novartis) in c-RPMI 1640 medium at 37° C. for 3 h, washed three times and incubated for 12 h. The GFP expression in the TCRγδ+CD3+ cell population was quantified by flow cytometry.
A strategy was developed to characterize the paired TCRγδ repertoire in humans. The primers were designed for all non-pseudogene TRGV and TRDV regions along with antisense primers for their respective constant regions. Two sets of primers (external and internal) were designed in order to perform a nested PCR (Table 1). The PCR products were examined by agarose gel electrophoresis before sequencing (
Establishment of Human TCRαβ and TCRγδ Retroviral Expression Clone Library
Many of the downstream applications of paired TCRαβ or TCRγδ sequence analysis require cloning and expression of the antigen specific receptors for immunological studies such as structural and functional characterization, biochemical characterization, epitope identification, and gene therapy18,29,30. Thus, a rapid cloning method was developed to improve on conventional restriction enzyme-mediated ligation techniques, which can be cumbersome and time consuming. In addition, use of restriction enzymes for cloning becomes problematic because of the potential occurrences of restriction sites in some variable regions and the non-germline CDR3 sequences of the TCR chains. The vector used for TCR expression is pMICherry, which has been successfully used to construct TCR clones for the generation of retrogenic mice31,32. A schematic diagram of the cloned TCR chains in the pMICherry vector is shown in
To clone full length TCR chains, a TRGV9/TRDV2 clone was chosen to demonstrate the feasibility of the cloning system, since the TRGV9/TRDV2 clonotype is dominant in the TCRγδ repertoire analysis from human PBMCs (
To test the functionality of the TCR clones that were made following the method described in
Effective TCR Activation Reporting by Nur77-GFP Jurkat 76 TCRα−β− Cells
An important application of TCR cloning and expression is to screen molecules that can activate or inhibit TCR signaling. Thus far, the common methods to detect TCR activation are using ELISA to detect cytokines (e.g. IFNγ) in the cell culture medium21,22, intracellular staining to report cytokine production by flow cytometry, or qRT-PCR to quantify the mRNA expression of cytokines, which are time-consuming, labor-intensive, and expensive. In the present invention, a TCR activation reporter cell line, Nur77-GFP Jurkat 76 TCRα−β− (NJ76 cells) was established by stably transducing Nur77-GFP BAC DNA into Jurkat 76 TCRα−β− cells. The Nur77-GFP reporting system has been demonstrated to reflect specific TCR signal strength by GFP expression40,41,42.
To test the functionality of NJ76 cells in reporting TCR activation, NJ76 cells were transfected with a murine KbPB1703-specific TCRαβ derived from influenza-infected mice along with a mouse CD3 construct. The KbPB1703+TCRαβ+ NJ76 cells (PB1-NJ76) were incubated with mouse splenocytes, the influenza PB1703 peptide, splenotytes and peptide, or mouse α-CD3/human α-CD28 as a positive control for 4 hours and GFP expression in transfected NJ76 cells was detected by flow cytometry (
This TCR-activation reporting system has also been tested for TCRγδ signaling. Zoledronic acid (Zometa, Novartis) is an aminobisphosphonate that has demonstrated antitumor effects via inhibition of tumor growth and angiogenesis and induction of malignant cell apoptosis in humans43,44,45. In addition, zoledronic acid can specifically stimulate and expand human TRGV9/TRDV2 cells46,47,48,49. Since it can result in the accumulation of upstream metabolites in the mevalonate pathway, e.g. IPP, which induce the expansion of γδ T cells in vitro and in vivo, zoledronic acid pre-treatment can increase the cytolysis of some cancer cell lines by γδ T cells50. After transfection of the human TRGV9/TRDV2 vector and human CD3 vector into NJ76 cells, the transfected TRGV9/TRDV2-NJ76 cells were pulsed with 50 μg/ml of zoledronic acid for 3 hours, and washed and incubated the cells at 37° C. for 12 h. The GFP expression level was quantified in transfected TRGV9/TRDV2-NJ76 cells and control cells by flow cytometry. The Nur77-GFP expression level is shown in
Effective TCR Activation Reporting by Nur77-Luc Jurkat 76 TCRα−β− Cells
Nur77-GFP BAC DNA was modified by using recombineering to substitute the GFP with firefly luciferase. In particular, recombineering was undertaken to insert a cassette with Luciferase-SV40pA-PGK-Neo-bGHpA into the Nur77 gene. A clone with such insertion (Nur77-Luc BAC DNA) was isolated and sequenced. TCRα−β− Jurkat 76 cells were transfected with the Nur77-Luc BAC DNA under a selectively complete RPMI medium with 500 μg/ml of Genetcin, yielding Nur77-Luciferase TCRα−β− Jurkat cells.
To determine optimum conditions for luciferase assays, tests of various numbers of Nur77-Luciferase TCRα−β− Jurkat cells per well were undertaken. In the tests, the cells were subjected to four hours of PMA/lonomycin stimulation followed by measurement in a luciferase reader. These values are shown in Table 5 under the column “Stimulated”. As a control, the luciferase reader was used to measure cells that were not stimulated. See Table 5, “Unstimulated” column. By comparison, the medium itself gave values of only 0 to 80 in the luciferase reader.
When assaying luciferase, using a cell number of 1×105 provides a four-fold rise in luciferase activity as compared with the unstimulated cells.
Rapid TCR Cloning by CDR3 Substitution Using Overlap Extension PCR and TCR Library
For TCRs, the only hypervariable regions are the CDR3 regions. Thus, cloning full length TCRs de novo for each application may expend unnecessary resources. To improve on this, a library was generated containing potential TRGV and TRDV “backbone” combinations that only require the swapping of individual CDR3 regions directly from PCR products. For example, in TRGV9/TRDV2 cells from PBMCs of healthy donors, the CDR3s of both γ and δ chains were found to be highly diverse (Table 4). To rapidly generate an array of TRGV9/TRDV2 clones with diverse CDR3γ and δ, a DNA linker, whose ends overlap with the TRGC and TRDV2 of the single cell PCR products, was designed. Similarly for other combinations of the TRGV/TRDV family several DNA linkers were designed. These DNA linkers contain the TRGC region, 2A and one of the TRDV regions, as is shown in
Tables 8-11: “Partial” V and C regions amplified depending on the target sequence. (Column “Region” discloses nucleotide sequence positions based on the IMGT reference database, see Lefranc, M. -P., The Immunologist, 7, 132-136 (1999) and www.imgt.org/IMGTScientificChart/Nomenclature/IMGT-FRCDRdefinition.html.)
The present invention is not to be limited in scope by the specific embodiments described herein. Indeed, various modifications of the invention in addition to those described herein will become apparent to those skilled in the art from the foregoing description. Such modifications are intended to fall within the scope of the appended claims.
All patents, applications, publications, test methods, literature, and other materials cited herein are hereby incorporated by reference in their entirety as if physically present in this specification.
This application is a U.S. National Phase of International Patent Application No. PCT/US2016/064735, filed on Dec. 2, 2016, which published as WO 2017/096239 A1 on Jun. 8, 2017, and claims priority to U.S. Provisional Patent Application Ser. No. 62/263,318, filed on Dec. 4, 2015, all of which are herein incorporated by reference in their entirety.
The invention was made with government support under grant AI107625 awarded by the National Institutes of Health. The government has certain rights in the invention.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US2016/064735 | 12/2/2016 | WO |
| Publishing Document | Publishing Date | Country | Kind |
|---|---|---|---|
| WO2017/096239 | 6/8/2017 | WO | A |
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| Number | Date | Country | |
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| 20190040381 A1 | Feb 2019 | US |
| Number | Date | Country | |
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| 62263318 | Dec 2015 | US |
