CN118355277A - Cell assays and methods for assessing MHC-peptide-TCR interactions and kinetics - Google Patents
Cell assays and methods for assessing MHC-peptide-TCR interactions and kinetics Download PDFInfo
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Abstract
The present invention provides compositions, systems and methods for quantifying the kinetics of binding rates to a receptor molecule and an MHC molecule. The generated quantitative data may have an accuracy and quantity suitable for generating the predictive model. More specifically, the assays described herein can be adapted for analysis of large amounts of MHC associated peptides.
Description
Cross Reference to Related Applications
The present application claims priority from the filing date of U.S. provisional patent application No. 63/287,012, filed on 7 at 12 at 2021, the disclosure of which is incorporated herein by reference in its entirety. The present application also claims priority from the filing date of U.S. provisional patent application No. 63/397,325 filed on 8/11 of 2022, the disclosure of which is incorporated herein by reference in its entirety.
Technical Field
The present specification relates generally to methods and assays for assessing major histocompatibility complex (pMHC) and T cell receptor interactions and kinetics of displayed peptides. More specifically, the present description relates to the use of cell-based assays to assess the binding kinetics of pMHC and receptors in the context of selection and activation.
Background
Accurate prediction of conditions that activate an adaptive immune response remains plagued for scientists and medical practitioners. No prior art can accurately predict how a subject will respond when applying immunotherapy techniques. For example, only 20% to 40% of patients respond to immunotherapy. In addition, existing drugs can sometimes activate various immune cells, and sometimes elicit autoimmune responses. Sharma P, hu-Lieskovan S, wargo JA, ribas a. Primary, adaptive and acquired resistance to cancer immunotherapy "Cell (Cell)" 2017, 2 months 9; 168 (4): 707-723.Doi:10.1016/j.cell.2017.01.017.pmid:28187290; PMCID: PMC5391692.
Understanding of the interactions and kinetics between Antigen Presenting Cells (APCs) and T cells is limited because various surface molecules of APCs interact with various surface molecules of T cells. Recently, it has also become apparent that some of these interactions may not replicate in vitro or non-living systems. For example, surface plasmon resonance-based assays fail to take into account factors that influence the binding kinetics associated with living cells. Tetramer staining is currently the gold standard for assessing T cell specificity, but comparable rate constant data related to binding kinetics cannot be collected. In addition, predictive models require a large amount of data, and such techniques require a significant amount of time.
Thus, there is a need for a cell-based assay to measure kinetics between Antigen Presenting Cells (APCs) and T cells in a manner that generates comparable data quickly and at low cost. Such assays will also result in higher response rates in patients while reducing the severity of or eliminating autoimmune responses. The present disclosure addresses these and other needs.
Disclosure of Invention
Aspects of the invention include a composition for use in a biological kinetic assay comprising: a polypeptide molecule comprising an antigen binding region; one or more fluorophores linked to the polypeptide molecule; and an antigenic peptide that binds to the antigen binding region of the polypeptide molecule.
Aspects of the invention include a composition for use in a biological kinetic assay comprising: a polypeptide molecule comprising an antigen binding region; one or more fluorophores linked to the polypeptide molecule; and an antigenic peptide that binds to the antigen binding region of the polypeptide molecule, wherein the antigenic peptide comprises UV cleavable amino acids.
In some embodiments, the polypeptide molecule comprises a single polypeptide chain. In some embodiments, the polypeptide molecule comprises a first polypeptide chain and a second polypeptide chain.
In some embodiments, the antigen binding region comprises at least a portion of a first polypeptide chain of a polypeptide molecule. In some embodiments, the first polypeptide chain comprises an α 1 domain and an α 2 domain. In some embodiments, the first polypeptide chain comprises an α 3 domain. In some embodiments, the first polypeptide chain comprises an amino acid sequence of a recombinant human leukocyte antigen. In some embodiments, the first polypeptide chain comprises the amino acid sequence of recombinant murine histocompatibility system 2. In some embodiments, the second polypeptide chain is linked to the α 3 domain of the first polypeptide chain. In some embodiments, the second polypeptide chain comprises the amino acid sequence of a β 2 -microglobulin molecule.
In some embodiments, the antigen binding region comprises at least a portion of a first polypeptide chain and at least a portion of a second polypeptide chain. In some embodiments, the portion of the first polypeptide chain comprises an α 1 domain, the portion of the second polypeptide chain comprises a β 1 domain, and the α 1 domain and the β 1 domain form an antigen binding region. In some embodiments, the first polypeptide chain further comprises an α 2 domain. In some embodiments, the second polypeptide chain further comprises a β 2 domain. In some embodiments, the first polypeptide chain comprises an amino acid sequence of a recombinant human leukocyte antigen. In some embodiments, the second polypeptide chain comprises a polypeptide sequence of a recombinant human leukocyte antigen. In some embodiments, the antigen binding region comprises at least one alpha-helix. In some embodiments, the antigen binding region comprises at least one β -sheet.
In some embodiments, one or more fluorophores are covalently linked to the polypeptide molecule. In some embodiments, the covalent bonding comprises an ester. In some embodiments, one or more fluorophores are covalently linked to one or more solvent-exposed surface lysine residues of the polypeptide molecule.
In some embodiments, the first polypeptide chain and the second polypeptide chain are non-covalently linked. In alternative and additional embodiments, the first polypeptide chain and the second polypeptide chain are covalently linked.
In some embodiments, the polypeptide molecule binds to an antigen presenting cell surrogate. In some embodiments, the antigen presenting cell replacement comprises a bead. In some embodiments, the polypeptide molecule is attached to the antigen presenting cell replacement via a linker. In some embodiments, the linker comprises a polyethylene glycol (PEG) molecule.
In some embodiments, the composition comprises a receptor that binds to an antigen binding region of a polypeptide molecule.
In some embodiments, the composition comprises living lymphocytes. In some embodiments, at least a portion of the receptor is located on the cell membrane of a living lymphocyte. In some embodiments, the composition comprises a co-receptor on the cell membrane of a living lymphocyte. In some embodiments, the co-receptor binds to a portion of the polypeptide molecule. In some embodiments, the living lymphocyte is a T cell and the receptor is a T Cell Receptor (TCR). In some embodiments, the co-receptor comprises a CD8 molecule. In some embodiments, the living lymphocyte is a B cell and the receptor is a B Cell Receptor (BCR). In some embodiments, the co-receptor comprises a CD4 molecule. In some embodiments, the living cells comprise macrophages and the receptors comprise chemokine receptors. In some embodiments, the living cells comprise dendritic cells and the receptors comprise Pattern Recognition Receptors (PRRs).
In some embodiments, the antigenic peptide ranges from 8 to 11 amino acid residues in length. In other embodiments, the antigenic peptide ranges from 15 to 24 residues in length. In some embodiments, the antigenic peptide comprises a UV cleavable moiety.
Aspects of the invention include a reaction mixture for generating a probe complex for use in a biological kinetic assay, the mixture comprising any of the compositions above and herein and a target antigen peptide.
In some embodiments, the target antigenic peptide is present in a molar excess concentration compared to the antigenic peptide bound to the antigen binding region of the polypeptide molecule. In some embodiments, the concentration of the target antigenic peptide is 25 times the concentration of the antigenic peptide.
In some embodiments, the reaction mixture comprises 25mM TRIS. In some embodiments, the pH of the reaction mixture is 8.0. In some embodiments, the reaction mixture comprises 150mM NaCl. In some embodiments, the reaction mixture comprises 4mM EDTA. In some embodiments, the reaction mixture comprises 5% ethylene glycol.
Aspects of the invention include methods of forming a monomeric probe complex comprising: contacting a polypeptide molecule comprising an antigen binding region with a first antigenic peptide to generate an antigen presenting complex; contacting the antigen presenting complex with a plurality of fluorophore molecules to generate a fluorophore-labeled antigen presenting complex; determining the amount of fluorophore molecules covalently bound to the fluorophore-labeled antigen presenting complexes; and exchanging the first antigenic peptide with the second antigenic peptide to generate a monomeric probe complex.
In some embodiments, the method of generating a monomeric probe complex includes exchanging a first antigenic peptide with a second antigenic peptide, including cleaving the first antigenic peptide to generate a cleaved first antigenic peptide. In some embodiments, the cleaved first antigenic peptide has a lower binding affinity for the antigen binding region than the first antigenic peptide. In some embodiments, the second antigenic peptide has a higher affinity for the antigen binding region than the cleaved first antigenic peptide.
In some embodiments, the method of generating a monomeric probe complex includes cleaving a first antigenic peptide, including the application of UV radiation. In some embodiments, the UV radiation comprises a wavelength of 365 nanometers.
In some embodiments, the step of contacting the antigen presenting complex with a plurality of fluorophore molecules to generate a fluorophore-labeled antigen presenting complex comprises covalently linking one or more solvent-exposed surface lysine residues of the polypeptide molecules to one or more of the fluorophore molecules.
In some embodiments, the method of generating a monomeric probe complex includes separating one or more unconjugated fluorophores from the labeled monomeric probe complex. In some embodiments, a method of generating a monomeric probe complex includes determining a concentration of a plurality of labeled monomeric probe complexes.
In some embodiments, the method of generating a monomeric probe complex includes determining an average number of fluorophores conjugated to each of the plurality of labeled monomeric probe complexes. In some embodiments, the step of determining an average number of fluorophores conjugated to each of the plurality of labeled monomeric probe complexes comprises using a plurality of relative abundance values, wherein each relative abundance value corresponds to a different number of conjugated fluorophores. In some embodiments, each of the plurality of relative abundance values is determined using mass spectrometry.
Aspects of the invention include methods for collecting association rate data to assess living cell activation, comprising: contacting a plurality of living cells with a plurality of compositions of any of the compositions described herein and above at a concentration, wherein each of the plurality of living cells comprises a plurality of receptor molecules on a cell membrane; binding a receptor molecule to the composition over a time interval to form a plurality of receptor-probe complexes, wherein each receptor-probe complex comprises a composition that binds to a receptor; collecting at least two samples of a plurality of living cells at different points in time within the time interval; contacting living cells in each of the at least two samples with an immobilization agent to preserve the receptor-probe complex and prevent further binding between the receptor molecules and the composition; determining the amount of receptor-probe complexes on the cell membrane of each cell; and analyzing the amount of receptor-probe complexes on the cell membrane of each cell in each sample to collect association rate data.
In some embodiments, the living cells comprise T cells. In some embodiments, the living cells comprise B cells. In some embodiments, the living cells comprise macrophages. In some embodiments, the living cells comprise dendritic cells.
In some embodiments, the signal strength is measured using an analysis device. In some embodiments, the analysis device comprises a flow cytometer. In some embodiments, the analysis device comprises a fluorometer.
In some embodiments, the fixative comprises paraformaldehyde. In some embodiments, the method comprises preventing receptor internalization by reducing the temperature of the receptor-probe complex. In some embodiments, the temperature is reduced to 4 ℃. In some embodiments, the method comprises isolating one or more unbound compositions from the plurality of living cells.
In some embodiments, each of the receptor-probe complexes comprises a CD8 molecule. In some embodiments, each of the receptor-probe complexes comprises a CD4 molecule.
Aspects of the invention include methods for collecting dissociation rate data to assess living cell activation, comprising: contacting a plurality of living cells with a plurality of any of the compositions described herein and above, wherein each of the plurality of living cells comprises a plurality of receptor molecules on a cell membrane, at a concentration; binding a receptor molecule to the composition to form a plurality of receptor-probe complexes until equilibrium is reached, wherein each receptor-probe complex comprises a composition that binds to a receptor; dissociating a portion of the receptor-probe complex over a time interval by reducing the concentration of the composition; collecting at least two samples of a plurality of living cells at different points in time within the time interval; contacting living cells in each of the at least two samples with an immobilization agent to preserve the receptor-probe complex and prevent further binding between the receptor molecules and the composition; determining the amount of receptor-probe complexes on the cell membrane of each cell; and analyzing the amount of receptor-probe complexes on the cell membrane of each cell in each sample to collect association rate data.
In some embodiments, the living cells comprise T cells. In some embodiments, the living cells comprise B cells. In some embodiments, the living cells comprise macrophages. In some embodiments, the living cells comprise dendritic cells. In some embodiments, the signal strength is measured using an analysis device. In some embodiments, the analysis device comprises a flow cytometer. In some embodiments, the analysis device comprises a fluorometer. In some embodiments, the fixative comprises paraformaldehyde.
In some embodiments, the method comprises preventing receptor internalization by reducing the temperature of the receptor-probe complex. In some embodiments, the temperature is reduced to 4 ℃.
In some embodiments, the method comprises isolating one or more unbound compositions from the plurality of living cells. In some embodiments, each of the receptor-probe complexes comprises a CD8 molecule. In some embodiments, each of the receptor-probe complexes comprises a CD4 molecule.
In some embodiments, the method further comprises permeabilizing the cell membrane of each cell. In some embodiments, the method further comprises applying a detection reagent for detecting the phosphorylation level of the intracellular domain of each of the living cells. In some embodiments, the intracellular domain comprises a zeta domain. In some embodiments, the detection reagent comprises an antibody.
Aspects of the invention include a system for measuring binding kinetics to assess living cell activation comprising: an analysis device comprising an analysis chamber. In some embodiments, the analysis chamber comprises a composition as described above and herein. In some embodiments, an analysis device comprises: a light source for interrogating the analysis chamber; and a detector for detecting the signal.
In some embodiments, the system further comprises a computer system comprising a non-transitory computer-readable storage medium, wherein the non-transitory computer-readable storage medium comprises instructions for analyzing the signal. In some embodiments, analyzing the signal includes normalizing the signal with respect to a previously determined calibration value.
In some embodiments, the analysis chamber comprises a flow cell. In some embodiments, the analysis device comprises a flow cytometer. In some embodiments, the analysis device comprises a fluorometer. In some embodiments, the analysis device comprises a microscope. In some embodiments, the analysis device comprises a mass spectrometer.
Aspects of the invention include a system for measuring binding kinetics to assess living cell activation comprising: an analysis device comprising an analysis chamber. In some embodiments, the analysis chamber comprises a reaction mixture as described above and herein.
In some embodiments, an analysis device comprises: a light source for interrogating the analysis chamber; and a detector for detecting the signal.
In some embodiments, the system further comprises a computer system comprising a non-transitory computer-readable storage medium, wherein the non-transitory computer-readable storage medium comprises instructions for analyzing the signal. In some embodiments, analyzing the signal includes normalizing the signal with respect to a previously determined calibration value.
In some embodiments, the analysis chamber comprises a flow cell. In some embodiments, the analysis device comprises a flow cytometer. In some embodiments, the analysis device comprises a fluorometer. In some embodiments, the analysis device comprises a microscope. In some embodiments, the analysis device comprises a mass spectrometer.
In one aspect, a method for collecting biophysical parameter data to evaluate a rate constant of association of a T Cell Receptor (TCR) with a peptide-Major Histocompatibility Complex (MHC) is described according to various embodiments. In various embodiments, the method includes generating a set of monomeric probes. In various embodiments, each monomeric probe comprises a detection molecule and one MHC comprising a peptide. In various embodiments, the method includes associating TCR molecules with monomeric probes in a one-to-one correspondence to form TCR-monomeric probe complexes over a period of time. In various embodiments, two or more subsets of TCR-monomer probe complexes are within the time interval. In various embodiments, each subgroup is acquired at a different point in time. In various embodiments, the method includes preventing the formation of new TCR-monomer probe complexes within each subgroup at their corresponding time points. In various embodiments, the method includes measuring the signal intensity from the detection molecules in each subset using an analytical device.
In one aspect, a method for collecting biophysical parameter data to evaluate a T Cell Receptor (TCR) dissociation rate constant with a peptide-major histocompatibility complex (pMHC) is described according to various embodiments. In various embodiments, the method includes generating a set of monomeric probes, wherein each monomeric probe comprises a detection molecule and one MHC comprising a peptide. In various embodiments, the method includes associating TCR molecules with monomeric probes in a one-to-one correspondence to form TCR-monomeric probe complexes. In various embodiments, the method includes dissociating the TCR-monomer probe complex into a monomer probe and a TCR over a time interval. In various embodiments, the method includes sampling two or more subsets of TCR-monomer probe complexes over the time interval. In various embodiments, each subgroup is acquired at a different point in time. In various embodiments, the method includes preventing dissociation of additional TCR-monomer probe complexes within each subgroup at their corresponding time points. In various embodiments, the method includes measuring the signal intensity from the detection molecules in each subset using a high throughput analysis device.
These and other aspects will be further explained in the remainder of this disclosure, including examples.
Incorporated by reference
All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference. To the extent publications and patents or patent applications incorporated by reference contradict the disclosure contained in this specification, this specification is intended to supersede and/or take precedence over any such contradictory material.
Drawings
The features of the present technology are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present technology will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the technology are utilized, and the accompanying drawings (also referred to herein as "Figure/fig.). The drawings are not intended to be drawn to scale. Like reference numbers and designations in the various drawings indicate like elements. For purposes of clarity, not every component may be labeled in every drawing. In the drawings:
figure 1 graphically illustrates T cell selection occurring in thymus according to various embodiments.
FIG. 2 is a schematic representation of polypeptide molecules of antigen presenting cells that bind to cell surface proteins of T cells, according to various embodiments.
FIG. 3 is a graph showing the intensity of association signals at different time points over a time interval for a cell-based assay for determining association or dissociation rates according to various embodiments.
Fig. 4 is a schematic diagram illustrating an example of lymphocyte and monomer probes according to various embodiments.
Fig. 5A is a flow chart of a process for collecting association rate data to assess living cell activation, according to various embodiments.
Fig. 5B is a flow chart of a process for association determination according to various embodiments.
FIG. 6A is a flowchart of a process for collecting dissociation rate data to assess living cell activation, according to various embodiments.
Fig. 6B is a flow chart of a process for dissociation determination according to various embodiments.
FIG. 7A is example data from a graphical format of association assays, according to various embodiments.
Fig. 7B is example data from a graphical format of association assays, in accordance with various embodiments.
FIG. 8A is example data from a graphical format of dissociation assays according to various embodiments.
FIG. 8B is example data from a graphical format of a dissociation determination according to various embodiments.
Fig. 9A is a diagram depicting a T cell receptor complex comprising multiple proteins located within a cell membrane, in accordance with various embodiments.
Fig. 9B is a diagram depicting CD8 complexes within a cell membrane, according to various embodiments.
Fig. 9C is a diagram depicting CD4 molecules located within a cell membrane, according to various embodiments.
Fig. 10A is a diagram depicting pMHC class I molecules comprising a polyprotein complex associated with a peptide located within a cell membrane, according to various embodiments.
Fig. 10B is a diagram depicting pMHC class II molecules comprising a polyprotein complex associated with a peptide located within a cell membrane, according to various embodiments.
FIG. 11 is a cellular pathway process of a peptide presentation pathway according to various embodiments.
Fig. 12 is a diagram of an exemplary method of generating MHC complexes comprising UV cleavable peptides according to various embodiments.
FIG. 13 is a diagram of an exemplary method of exchanging UV cleavable peptides with a peptide of interest according to various embodiments.
FIG. 14 is a schematic diagram of a system for measuring binding kinetics to assess living cell activation, in accordance with various embodiments.
It should be understood that the drawings are not necessarily drawn to scale and that the objects in the drawings are not necessarily drawn to scale relative to each other. The accompanying drawings are illustrations that are intended to provide a clear and thorough understanding of the various embodiments of the apparatus, systems, and methods disclosed herein. Wherever possible, the same reference numbers will be used throughout the drawings to refer to the same or like parts. Furthermore, it should be understood that the drawings are not intended to limit the scope of the present teachings in any way.
Detailed Description
The present specification describes various embodiments of techniques for assessing ligand (e.g., major histocompatibility complex displaying peptide [ pMHC ], co-receptors [ e.g., CD4, CD 8), etc. ] and receptor (e.g., T cell receptor [ TCR ], B cell receptor [ BCR ], etc.) interactions and kinetics. Such techniques enable researchers and medical practitioners to optimize binding interactions and kinetics to obtain the desired adaptive immune response. However, the present disclosure is not limited to these exemplary embodiments and applications nor to the exemplary embodiments and application operations or the manner described herein. Furthermore, the figures may show simplified or partial views, and the dimensions of elements in the figures may be exaggerated or not to scale.
In addition, where a list of elements (e.g., elements a, b, c) is referred to, such reference is intended to include any one of the elements listed alone, any combination of less than all of the elements listed, and/or a combination of all of the elements listed. The division of the sections in the specification is merely for ease of examination and does not limit any combination of the elements in question.
When values are described as ranges, it is to be understood that such disclosure includes all possible sub-ranges disclosed within such ranges, as well as specific values falling within such ranges, whether specifically indicated as being specific values or specific sub-ranges.
It should be understood that any use of the subtitles herein is for organizational purposes and should not be construed as limiting the application of those subtitle features to the various embodiments herein. Each feature described herein is applicable to and useable in all of the various embodiments discussed herein, and all features described herein can be used in any contemplated combination, regardless of the particular example embodiments described herein. It should also be noted that the exemplary description of specific features is primarily for the purpose of providing information and is not in any way limiting the design, sub-features, and functionality of the specifically described features.
Unless defined otherwise, scientific and technical terms used in connection with the present teachings described herein shall have the meanings commonly understood by one of ordinary skill in the art. Furthermore, unless the context requires otherwise, singular terms shall include the plural and plural terms shall include the singular. Generally, the terms and techniques described herein used in connection with chemistry, biochemistry, molecular biology, pharmacology, and toxicology are those available and commonly used in the art.
Definition:
The term "amino acid" as used herein generally refers to a group of carboxy alpha-amino acids, which may be encoded by a nucleic acid directly or in precursor form. A single amino acid is encoded by a nucleic acid consisting of three nucleotides, the so-called codon or base triplet. Each amino acid is encoded by at least one codon. This is called "degeneration of the genetic code". The term "amino acid" as used in the present application means a naturally occurring carboxy alpha-amino acid comprising: alanine (three-letter code: ala, one-letter code: A), arginine (arg, R), asparagine (asn, N), aspartic acid (asp, D), cysteine (cys, C), glutamine (gln, Q), glutamic acid (glu, E), glycine (gly, G), histidine (his, H), isoleucine (ile, I), leucine (leu, L), lysine (lys, K), methionine (met, M), phenylalanine (phe, F), proline (pro, P), serine (ser, S), threonine (thr, T), tryptophan (trp, W), tyrosine (tyr, Y), and valine (val, V).
According to various embodiments, the term "antigen" may be used interchangeably with "peptide" and may be associated with the Major Histocompatibility Complex (MHC). In various embodiments, MHC may display peptides for recognition by appropriate lymphocytes (e.g., T cells, B cells). In some embodiments, the kinetics of binding between MHC and a receptor (e.g., T cell receptor [ TCR ] or B cell receptor [ BCR ]) can vary based on the nature of the peptide (e.g., peptide sequence, secondary structure, tertiary structure, and higher structure). In various embodiments, the peptide may comprise a polymer of amino acids.
The term "antigen presenting cell" as used herein generally refers to a cell that is capable of presenting antigen in some manner. Antigen Presenting Cells (APCs) may include professional APCs and non-professional APCs.
Professional APCs may present antigen exclusively to T cells. In various embodiments, professional APCs can include macrophages, B cells, and dendritic cells. Professional APCs can internalize pathogens or foreign particles (e.g., cancer cells, bacterial cells, etc.) by phagocytosis (e.g., macrophages) or by receptor-mediated endocytosis (B cells). In some cases, the pathogen or foreign particle may be processed by proteolysis, and the resulting peptide fragment (e.g., antigen) may be combined with an MHC molecule to form an MHC complex. MHC complexes including peptide fragments can then migrate to the cell membrane and be displayed on its surface for T cell recognition and interaction. Professional APCs can generally include costimulatory molecules and MHC class II. Non-limiting examples of professional APCs include dendritic cells, macrophages and B cells.
Non-professional APCs can include all nucleated cell types of the subject. In some cases, non-professional APCs may include MHC class I molecules coupled to β -2 microglobulin to display endogenous peptides on their cell membrane.
The term "bead" as used herein generally refers to a particle. The beads may be solid or semi-solid particles. The beads may be gel beads. The gel beads may include a polymer matrix (e.g., a matrix formed by polymerization or cross-linking). The polymer matrix may include one or more polymers (e.g., polymers having different functional groups or repeating units). The polymers in the polymer matrix may be randomly arranged, such as in a random copolymer, and/or have an ordered structure, such as in a block copolymer. Crosslinking may be via covalent, ionic or induced, interactions or physical entanglement. The beads may be macromolecules. Beads may be formed from nucleic acid molecules that bind or hybridize together. Beads may be formed by covalent or non-covalent assembly of molecules (e.g., macromolecules), such as monomers or polymers. Such polymers or monomers may be natural or synthetic. Such polymers or monomers may be or include, for example, nucleic acid molecules (e.g., DNA or RNA). The beads may be formed of a polymeric material. The beads may be magnetic or non-magnetic. The beads may be rigid. The beads may be flexible and/or compressible. The beads may be destructible or dissolvable. The beads may be solid particles (e.g., metal-based particles including, but not limited to, iron oxide, gold, or silver) covered with a coating comprising one or more polymers. Such a coating may be destructible or dissolvable.
In various embodiments, the beads may be a sub-category of solid support. Other solid supports may include the surface of a plate (e.g., the surface of a well of a 96-well plate), the surface of a vial, the surface of a microscope slide, and the like. In some embodiments, the surface may be chemically treated to interact with the receptor and/or co-receptor.
The term "binding affinity" as used herein generally refers to the strength of the sum of the non-covalent interactions between a single binding site of a molecule (e.g., TCR or BCR) and its binding partner (e.g., pMHC). As used herein, unless otherwise indicated, "binding affinity" refers to an intrinsic binding affinity that reflects a 1:1 interaction between members of a binding pair (e.g., pMHC and TCR, pMHC and BCR). In various embodiments, the affinity of a molecule X for its partner Y may generally be represented by a dissociation constant (Kd). In various embodiments, the affinity of a molecule X for its partner Y may generally include a residence time. In some embodiments, the affinity of a molecule X for its partner Y may be generally expressed by a dissociation constant (Kd). In some embodiments, the affinity of a molecule X for its partner Y may generally include the rate of complex formation. In some embodiments, the affinity of a molecule X for its partner Y may be generally represented by a dissociation constant (Kd) and an association constant (Ka). In some embodiments, the affinity of a molecule X for its partner Y may be generally expressed as the frequency and duration of interaction.
The term "binding site" is interchangeable with the term "antigen binding region" and as used herein generally refers to a moiety that can specifically bind to a target (e.g., pMHC). Exemplary binding sites may include peptides, antibody fragments, domain antibodies, or variable domains of single chain antibodies. In some embodiments, the TCR comprises a binding site. In some embodiments, the BCR comprises a binding site. The antigen binding site may be a naturally occurring binding site or an engineered antigen binding site. Exemplary engineered antigen binding sites are DARPIN, domain-exchanged antibodies or domain-exchanged antibody fragments, and double variable domain antibodies.
The term "biological particle" as used herein generally refers to a discrete biological system derived from a biological sample. The biological particles may be macromolecules. The biological particles may be small molecules. The biological particle may be a virus. The biological particles may be cells or derivatives of cells. The biological particles may be organelles. The biological particle may be a nucleus. The biological particles may be rare cells in a population of cells. The biological particles may be any type of cell including, but not limited to, prokaryotic cells, eukaryotic cells, bacteria, fungi, plant, mammalian or other animal cell types, mycoplasma, normal tissue cells, tumor cells, or any other cell type, whether derived from single-cell or multicellular organisms. The biological particles may be a component of a cell. The biological particles may be or may include DNA, RNA, organelles, proteins, or any combination thereof. The biological particles may be or include a matrix (e.g., a gel or polymer matrix) that comprises cells or one or more components from cells (e.g., cell beads), such as DNA, RNA, organelles, proteins, or any combination from cells. The biological particles may be obtained from a tissue of a subject. The biological particles may be hardened cells. Such hardened cells may or may not include cell walls or cell membranes. The biological particles may include one or more components of the cell, but may not include other components of the cell. Examples of such components are nuclei or organelles. The cells may be living cells. Living cells can be cultured, for example, when encapsulated in a gel or polymer matrix, or when comprising a gel or polymer matrix.
As used herein, the term "biophysical parameter data" may include any measurement or observation of or associated with a biological particle. In some embodiments, the biophysical parameter data may include any measurement or characteristic of or associated with binding kinetics (e.g., T cells: pMHC and/or B cells: pMHC rate and rate constant).
As used herein, the terms "comprises/comprising", "containing/containing", "having/having", "including/including" and their variants are not intended to be limiting, are inclusive or open ended, and do not exclude additional, unrecited additives, components, integers, elements or method steps. For example, a process, method, system, composition, kit, or apparatus that comprises a list of features is not necessarily limited to only those features, but may include other features not expressly listed or inherent to such process, method, system, composition, kit, or apparatus.
The term "dilution buffer" generally refers to a buffer that can increase the volume of a sample. In various embodiments, the dilution buffer can increase the sample volume by 1, 2, 3, 4, 5, 6,7, 8, 9, 10, 15, 20, 25, 50, 75, or 100 times the original sample volume. In some embodiments, the dilution buffer may include the same chemistry as the buffer containing the sample.
The terms "fixative" and "fixation buffer" are used interchangeably and generally refer to an agent that can hold cells in a particular state for examination. In various embodiments, the immobilization buffer may prevent degradation. In some embodiments, a fixed buffer may be used for the sampling step. In some embodiments, a fixation buffer may be used to terminate the reaction (e.g., pMHC and TCR interactions and/or pMHC and BCR interactions). According to some embodiments, a 4% Paraformaldehyde (PFA) solution in Phosphate Buffered Saline (PBS) may be used as the fixation buffer.
The terms "coupled," "linked," "conjugated," "associated," "attached," "linked" or "fused" as used herein are used interchangeably and generally refer to the attachment or linking (e.g., chemical binding) of one molecule (e.g., polypeptide, receptor, analyte, etc.) to another molecule (e.g., polypeptide, receptor, analyte, etc.). In various embodiments described herein, the linking comprises covalent or non-covalent linking.
As used herein, the term "linker" may be used interchangeably with the term "spacer" and refers to an inert polymer that can hold two or more molecules together. In various embodiments, the linker may function to keep the two molecules away from each other. In various embodiments, the linker length may be selected for a particular application. In various embodiments, the linker may comprise polyethylene glycol (PEG), poly (N-vinylpyrrolidone) (PVP), polyglycerol (PG), poly (N- (2-hydroxypropyl) methacrylamide) (PHPMA), polyoxazoline (POZ), biotin, avidin, streptavidin, or any other known or useful non-reactive molecule capable of linking two or one other molecules together. As used herein, a linker may be used to link an oligonucleotide to a cleavable substrate.
As used herein, the term "major histocompatibility complex" ("MHC") generally refers to a group of proteins on the cell surface that play a role in the immune response. The function of an MHC molecule may be to bind peptide fragments derived from a pathogen and display them on the cell surface. As used herein, the term "pMHC" generally refers to peptides complexed with MHC. In various embodiments, the MHC comprises MHC class I. In various embodiments, the MHC comprises MHC class II.
As used herein, the term "plurality (ones)" means more than one.
The term "plurality" as used herein may be 2, 3, 4, 5, 6, 7, 8, 9, 10 or more.
As used herein, the term "detection molecule" generally means any substance that can generate a signal or be detected. More specifically, the detection molecule may comprise a fluorescent molecule. In some embodiments, the detection molecule may comprise a fluorescent molecule that does not degrade when subjected to an immobilization process (e.g., a process using an immobilization buffer). The detection molecule may be exogenous or endogenous. The detection molecule may be coupled to a macromolecular component such as a protein, antibody, aptamer or amino acid using enzymatic, chemical or other known labeling methods. The detection molecule may be coupled to a biotinylated structure (e.g., avidin, streptavidin, biotin). The detection molecule may be coupled to a bead.
In various embodiments, the detection molecule may comprise a NHS-ester fluorophore. In many embodiments, the NHS-ester fluorophore can be covalently conjugated to a solvent-exposed surface lysine residue of an amino acid sequence. Such amino acid sequences may be sequences of MHC molecules (e.g., MHC class I or MHC class II). The fluorescent molecules used herein may be selected to measure probes that bind to TCR or BCR. In various embodiments, the fluorophore may be selected based on its resistance to UV radiation.
As used herein, the term "substantially" means sufficient to achieve the intended purpose. Thus, the term "substantially" allows minor, insignificant changes to absolute or ideal conditions, dimensions, measurements, results, etc., as would be expected by one of ordinary skill in the art, without significantly affecting overall performance. When used with respect to a numerical value or a parameter or characteristic that may be expressed as a numerical value, substantially means within ten percent.
The term "variable" as used in connection with T Cell Receptor (TCR) and B Cell Receptor (BCR) means that certain portions of the TCR and BCR variable domains differ greatly in sequence between TCR and BCR, and are used for the binding and specificity of each particular TCR and BCR for its particular peptide (e.g., peptide associated with MHC class I, peptide associated with MHC class II). However, the variability is not evenly distributed throughout the variable domains of TCRs and BCRs. It is concentrated in three segments called hypervariable regions in the light and heavy chain variable domains. The more conserved portions of the variable domains are called Framework Regions (FR). The variable domains of the natural heavy and light chains each comprise four FR, which are connected by three hypervariable regions, mainly in the β -sheet configuration, which form loops connecting the β -sheet structure and in some cases form part of the β -sheet structure. The hypervariable regions in each strand are held tightly together by the FR and together with the hypervariable regions from the other strand contribute to the formation of the antigen/pMHC binding site.
As used herein, the term "hypervariable region" refers to the amino acid residues in a TCR, BCR, or antibody that are responsible for antigen/pMHC binding. Hypervariable regions typically comprise amino acid residues from "complementarity determining regions" or "CDRs" and/or those residues from "hypervariable loops. In some embodiments, "CDR" means the complementarity determining region of a TCR, BCR, or antibody. "framework region" or "FR" residues are those variable domain residues other than the hypervariable region/CDR residues as defined herein.
Unless defined otherwise, scientific and technical terms used in connection with the present teachings described herein shall have the meanings commonly understood by one of ordinary skill in the art. Furthermore, unless the context requires otherwise, singular terms shall include the plural and plural terms shall include the singular. In general, the terms and techniques described herein used in connection with cell and tissue culture, molecular biology, and protein and oligonucleotide or polynucleotide chemistry and hybridization are those available and commonly used in the art. Standard techniques are used for example for nucleic acid purification and preparation, chemical analysis, recombinant nucleic acid and oligonucleotide synthesis. Enzymatic reactions and purification techniques are performed according to manufacturer's instructions or as commonly done in the art or as described herein. The techniques and procedures described herein are generally performed according to conventional methods well known in the art and as described in various general and more specific references cited and discussed throughout the present specification. See, e.g., sambrook et al, molecular cloning: laboratory manual (third edition, cold spring harbor laboratory Press, new York Cold spring harbor, 2000). The terms and techniques described herein used in connection with laboratory procedures and techniques are those available and commonly used in the art.
I. Summary of the invention
The immune system has the ability to detect abnormalities and protect the host organism from high responses. High detectability can be achieved by highly variable Complementarity Determining Regions (CDRs) of the α and β chains or the δ and γ chains of the TCR interacting with the peptide-major histocompatibility complex (pMHC). In various embodiments, the CDRs combined with the peptide sequences of pMHC may contribute significantly to the TCR: pMHC binding affinity. The assays described herein can quantitatively measure TCR in a high throughput manner: pMHC and BCR: pMHC binding event.
With reference to fig. 1, the concept of positive and negative selection of lymphocytes (e.g., T cells) in the thymus is described. During T cell maturation, only a small fraction of T cells are positively selected. When T Cell Receptors (TCRs) of T cells have little affinity for the host/self pMHC located in the thymus, these T cells will be negatively selected and die by disregarding (e.g., they will not continue the maturation process). When T cells have a high affinity for host/self pMHC located in thymus, these T cells will be negatively selected and destroyed by apoptosis. Positively selected T cells include TCRs that can bind to host/self pMHC within a tolerable range of affinities. Depicted in fig. 1 is what is known as the affinity threshold hypothesis, and thymus selection depends on the affinity of T cell receptors for self pMHC. Thus, the life system can generate T cells that are largely self-tolerant and still be able to identify and clear foreign intruders (e.g., viruses and cancer cells).
In various organisms, TCR diversity can be produced by genetic recombination of DNA coding segments in single-body T cells using a mechanism called somatic V (D) J recombination by RAG1 and RAG2 recombinases. In various embodiments, V (D) J recombination occurs in developing T cells during the early stages of thymus maturation. In some embodiments, V (D) J recombination may be an essential feature of an adaptive immune response. BCR diversity can be generated in a variety of organisms using similar recombinant methods.
In humans and other mammals, V (D) J recombination can occur in lymphoid organs. In various embodiments, the lymphoid organ may comprise thymus. In various biological systems, V (D) J recombination can rearrange variable (V), linkage (J), and in some cases diversity (D) gene segments almost randomly. In various embodiments, V (D) J recombination may result in modification of CDR regions. In some embodiments, V (D) J recombination can produce CDRs comprising the new amino acid sequence.
The positively selected T cells can then be moved throughout the host organism as part of an adaptive immune response. Referring to fig. 2, interactions between cell surface proteins 210 (e.g., receptors, TCRs) of T cells 214 and cell surface proteins (e.g., antigen peptides 208, such as pMHC, that bind to antigen binding region 206 of polypeptide molecule 204) of other cells (e.g., antigen presenting cells 202) help determine whether T cells 214 are positively selected and subsequently activated to destroy the bound cells. In some embodiments, a co-receptor 212 of T cell 214, such as CD4 or CD8, may bind to a region of polypeptide molecule 204 to aid in the selection process. This interaction may be particularly important because it may be involved in the ability of T cells 214 to recognize host cells (e.g., themselves) from invading or malignant cells (see positive selection above). Specifically, the total number of TCR interactions that occur over a period of time may determine the T cell response.
Host cells typically express Major Histocompatibility Complexes (MHC) on their cell surfaces, each of which may include peptides for T cell recognition. In particular, T cells may include T Cell Receptors (TCRs) on their surface that can recognize MHC molecules of other cells. MHC peptides play a role in determining the association rate and dissociation rate (e.g., binding affinity) of MHC/TCR complexes that modulate adaptive immune responses.
In the natural system, peptides bound to MHC molecules are produced mainly by proteasome degradation of cytoplasmic proteins. Thereafter, MHC: the peptide complex may be inserted into the outer plasma membrane through the endoplasmic reticulum. Thus, MHC molecules function to display intracellular proteins to cytotoxic T cells.
Healthy cells will exhibit peptides from normal cellular protein turnover, and T cells will not be activated. However, when the cell expresses a foreign protein (e.g., a protein derived from a viral infection), the cell is specific for MHC: the peptide complex specific TCR will recognize and cause cell death.
Cell-based assays are useful because some parameters that control association and dissociation rates can depend on living cell interactions. Non-limiting examples of such dependencies include binding more tightly captured bonds and slipping bonds that break under force when force is applied. Thus, cell-based assays may perform better than in vitro assays. Current cell-based protocols (e.g., tetramer staining) are typically low-throughput and do not produce rate constant related data. In particular, associating a single MHC molecule with a single fluorophore or a known number of fluorophores allows quantitative data to include rate binding information, as it allows for the study of pMHC in the presence of co-receptors within the cell membrane: receptor interactions. For these and other reasons, cell-based assays are well suited for studying pMHC: TCR and/or pMHC: binding kinetics and interactions between BCR and other ligand-receptor binding kinetics and interactions. The present disclosure includes assays and methods for rapidly and accurately measuring data to determine association and dissociation rate constants.
II composition
The present invention provides compositions for use in a biological kinetic assay. Examples of compositions may include a polypeptide molecule having an antigen binding region and an antigenic peptide that binds to the antigen binding region of the polypeptide molecule to which one or more fluorophores are attached. Another example of a composition may include a polypeptide molecule comprising an antigen binding region, one or more fluorophores linked to the polypeptide molecule, and an antigenic peptide bound to the antigen binding region of the polypeptide molecule, wherein the antigenic peptide comprises a UV cleavable amino acid.
In various embodiments, the polypeptide molecule may comprise a single polypeptide molecule (e.g., a first polypeptide chain). In alternative embodiments, the polypeptide molecule may comprise two or more polypeptide molecules. In many embodiments, the polypeptide molecules can include a first polypeptide molecule (e.g., a first polypeptide chain) and a second polypeptide molecule (e.g., a second polypeptide chain).
Major Histocompatibility Complex (MHC) I
Aspects of the T cell immune response include T cell recognition of peptides (e.g., antigens). In various embodiments, the effect of the Major Histocompatibility Complex (MHC) may be to mobilize peptides to the cell surface for TCR recognition by T cells (e.g., cytotoxic T cells).
Referring to fig. 10, according to various embodiments, peptides: MHC class I (pMHC I) 1000 is shown embedded within cell membrane 1020. In many embodiments, pMHC class I1000 may comprise a first polypeptide chain and a second polypeptide chain. The first polypeptide chain can include an alpha chain (e.g., alpha 1 1004、α2, 1006 and alpha 3 1008). The second polypeptide chain may include a β chain 1010. In various embodiments, pMHC class I1000 may comprise peptide 1002, which may act as a peptide that acts as an antigen. In various compositions, the alpha and beta chains 1010 may be associated using non-covalent bonds. In some compositions, the alpha and beta chains 1010 may be associated using covalent bonds. In various compositions, the alpha chain may comprise the amino acid sequence of a recombinant human leukocyte antigen. In some compositions, the α chain may comprise the amino acid sequence of recombinant murine histocompatibility system 2.
In various embodiments, the alpha chain can comprise about 350 amino acids and include three globular domains 1004, 1006, 1008. In various embodiments, three globular domains may be designated as α 1 1004、α2 1006 and α 3.
In various embodiments, the N-terminus of the alpha chain may be located in the alpha 1 1004 globular domain. In various embodiments, α 1 and α 2 1006 can be located in an extracellular compartment (e.g., within extracellular fluid). In some embodiments, α 1 and α 2 1006 may each comprise about 90 amino acids. In various embodiments, α 2 1006 may contain a 63 amino acid loop and disulfide bonds may be used to promote formation. In various embodiments, α 1 and α 2 can interact to form an antigen binding region of pMHC 1000.
In various compositions, the antigen binding region can comprise at least a portion of a first polypeptide chain (e.g., an alpha chain) of a polypeptide molecule. In other compositions, the first polypeptide chain can include an α 1 domain and an α 2 domain.
In various embodiments, the α chain may comprise α 3 1008, which may include a transmembrane segment 1012 that anchors pMHC 1000 to cell membrane 1020. In some embodiments, the transmembrane segment 1012 may comprise 26 amino acids. In some embodiments, α 3 1008 may contain disulfide bonds surrounding 86 amino acids to form a loop structure. In many compositions, the first polypeptide chain can include an α 3 domain.
In various embodiments, the α 3 1008 globular domain can interact with a co-receptor (e.g., a CD8 co-receptor of a T cell). In some embodiments, the α 3 -co-receptor interaction can hold pMHC class I1000 in place and the TCR on the cell membrane surface of the T cell can bind the α1- α2 heterodimeric ligand. In some embodiments, the α3-CD8 interaction may allow the α1- α2 heterodimeric ligand to interrogate the MHC associated peptide for antigenicity. In various embodiments, the C-terminus of the alpha chain may be located in the alpha 3 1004 globular domain. In some assays described herein, blocking anti-CD 8 antibodies may be used.
The cytoplasmic tail of CD8 can interact with Lck (lymphocyte-specific protein tyrosine kinase), and Lck can phosphorylate the cytoplasmic portion of CD3 and the zeta-chain (also referred to herein as zeta domain) of the TCR complex. Phosphorylation of CD3 and zeta-chains can lead to activation of a variety of transcription factors (e.g., NFAT, NF- κb, and AP-1), ultimately affecting expression of certain genes downstream of the signaling cascade.
In various compositions, the second polypeptide chain can be linked to the first polypeptide chain as described herein. For example, a second polypeptide chain (e.g., β chain 1010) can be linked to α 3 of the first polypeptide. In various embodiments, the β chain 1010 of pMHC class I may comprise a disulfide ring. In various embodiments, β strand 1010 can interact non-covalently with the α 3 1008 globular domain.
Referring to fig. 11, an exemplary process of peptide presentation pathway 1100. In various embodiments, MHC class I molecules may bind antigen molecules (e.g., peptides) and then the entire complex may be mobilized to the cell surface. In some embodiments, peptide 1110 can range from eight amino acids to about ten amino acids. In other embodiments, the peptide may comprise more than 10 amino acids.
In various embodiments, MHC class I1116 may bind to peptide 1110 derived from intracellular protein 1106 and display peptide 1110 for recognition by T cells external to cell 1102. Under some naturally occurring conditions, the source of intracellular protein 1106 may comprise viral proteins previously entered into the cell. Under other naturally occurring conditions, the source of intracellular protein 1106 may comprise a protein derived from an infected cell. In alternative cases, the source of intracellular protein 1106 may comprise a protein from a cancer cell. In some embodiments, the source of intracellular protein 1106 may comprise proteins from healthy cells and will not normally generate an immune response unless the host organism suffers from an autoimmune disease or some other affliction.
In various biological systems, proteasome 1108 comprises a protein complex capable of degrading a protein by proteolysis. In various embodiments, proteasome 1108 can use a protease to break peptide bonds of intracellular protein 1106 to produce peptide 1110.
In various biological systems, a transporter associated with the antigen processing complex (TAP) 1112 can deliver cytoplasmic peptides into the endoplasmic reticulum 1116. In some embodiments, the TAP 1112 structure may comprise two proteins (e.g., TAP-1 and TAP-2).
In some aspects of the process of peptide presentation pathway 1100, the TAP 1112 transporter can be associated with a peptide-loaded complex. In some embodiments, the peptide-loaded complex may comprise β 2 microglobulin (e.g., MHC chain), calreticulin, ERp57, TAP 1112, tapasin, and MHC molecules (e.g., MHC class I). In some embodiments, the peptide-loaded complex may hold MHC molecules in place until they associate with peptide 1112, thereby forming pMHC 1116. In various compositions, the second polypeptide chain (e.g., β chain) may comprise the sequence of a β 2 microglobulin molecule.
In various embodiments, the peptide presentation pathway 1100 may comprise a secretory pathway, in which pMHC 1116 may move to golgi 1118. In some embodiments, golgi 1118 may package pMHC 1116 into secretory vesicles 1120 for further transport.
In various embodiments, a secretory vesicle 1120 containing pMHC 1116 may fuse to the cell membrane 1104 of the cell 1102 and present the peptide 1110 to the extracellular space for T cell recognition.
Major Histocompatibility Complex (MHC) II
Aspects of the T cell immune response include T cell recognition of peptides (e.g., antigens). In various embodiments, the effect of the Major Histocompatibility Complex (MHC) may be to mobilize peptides to the cell surface for TCR recognition by T cells (e.g., helper T cells).
Referring to fig. 10B, peptide-MHC class II (pMHC II) 1050 is shown embedded within cell membrane 1020, according to various embodiments. In many embodiments, pMHC class II 1050 may comprise a first polypeptide chain and a second polypeptide chain. The first polypeptide chain can include an alpha chain (e.g., alpha 1 1054 and alpha 2 1060). The second polypeptide chain may include a beta chain (e.g., beta 1 1056 and beta 2 1058). In various embodiments, pMHC class II 1050 may comprise peptide 1052, which may act as a peptide that acts as an antigen. In various compositions, the alpha and beta chains may be associated using non-covalent bonds. In some compositions, the alpha and beta chains may be associated using covalent bonds. In various compositions, the alpha chain may comprise the amino acid sequence of a recombinant human leukocyte antigen.
In various embodiments, the alpha chain includes two globular domains 1054, 1060. In various embodiments, two globular domains may be designated as α 1 1054 and α 2 1060.
In various embodiments, the β chain includes two globular domains 1056, 1068. In various embodiments, two globular domains may be designated as α 1 1054 and α 2 1060.
In various embodiments, the N-terminus of the alpha chain may be located in the alpha 1 1054 globular domain. In various embodiments, β 1 1056 and β 2 1058 may be located in extracellular compartments (e.g., within extracellular fluids).
In various compositions, the antigen binding region can comprise at least a portion of a first polypeptide chain (e.g., an alpha chain) and at least a portion of a second polypeptide chain (e.g., a beta chain) of the polypeptide molecule.
In various embodiments, the α chain may comprise α 2 1060, which may include a transmembrane segment 1064 that anchors pMHC class II 1050 to cell membrane 1020. In various embodiments, the β chain may comprise β 2, 1058, which may include a transmembrane segment 1062 that anchors pMHC class II 1050 to cell membrane 1020.
In various embodiments, a co-receptor (e.g., a CD4 molecule) can interact with the β 2 domain of an MHC class II molecule through its D 1 domain.
The cytoplasmic tail of CD4 can interact with Lck (lymphocyte-specific protein tyrosine kinase), and Lck can phosphorylate the cytoplasmic portion of CD3 and the zeta-chain of the TCR complex. Phosphorylation of CD3 and zeta-chains can lead to activation of a variety of transcription factors (e.g., NFAT, NF- κb, and AP-1), ultimately affecting expression of certain genes downstream of the signaling cascade.
In various compositions, the second polypeptide chain can be linked to the first polypeptide chain as described herein. For example, a second polypeptide chain (e.g., a β chain) can be linked to a first polypeptide (e.g., an α chain).
T Cell Receptor (TCR)
Aspects of the adaptive immune response system include T cells, including membrane-associated TCRs. In some embodiments, the adaptive immune response comprises CD28 for providing a co-stimulatory signal. Referring to fig. 9A, a T Cell Receptor (TCR) -CD3 complex 900 embedded in a T cell membrane 950 is shown. In various embodiments, the TCR-CD3 complex 900 can comprise a disulfide-linked membrane-anchored heterodimeric protein. In many embodiments, the disulfide-linked membrane-anchored heterodimeric protein can comprise an alpha chain 902 and a beta chain 904. In various embodiments, the TCR-CD3 complex 900 may comprise surrogate receptors formed by gamma and delta chains. In various embodiments, the TCR-CD3 complex 900 a chain 902 and β chain 904 form the structure of an antigen binding site (e.g., pMHC binding site 906).
In various T cell conformations, the alpha chain 902 can comprise two extracellular domains, including a variable region 908 and a constant region 910. In various embodiments, β chain 904 may comprise two extracellular domains, including a variable region 912 and a constant region 914. In some conformations, the constant regions 910, 914 may be adjacent to the cell membrane 950. In some conformations, the variable regions 908, 912 can form a pMHC binding site 906 and can bind pMHC.
Each of the TCR chains 902, 904 can comprise a variable region 908, 912, and each variable region 908, 912 can comprise three hypervariable regions or Complementarity Determining Regions (CDRs). In some embodiments, CDR1, CDR2, and CDR3 may be discontinuously arranged on the amino acid sequence of the variable domains 908, 912 of TCR 900. In some embodiments, CDR3 may be the primary region of a processed antigenic peptide for recognition of pMHC.
Aspects of the immune response may require TCR-CD3 complex 900 to transmit signals that cause T cell activation. In various embodiments, CD3 molecules 916, 918 each have a longer cytoplasmic tail than alpha chain 902 and beta chain 904 to allow signal transduction to occur. In various embodiments, the TCR-CD3 complex 900 comprises a first CD3 molecule 916 comprising a gamma chain associated with an epsilon chain. In various embodiments, the TCR-CD3 complex 900 comprises a second CD3 molecule 918 comprising a delta chain associated with an epsilon chain.
In various embodiments, TCR-CD3 complex 900 ζ chain 920 may couple peptide recognition to several intracellular signaling pathways, including T cell activation.
Referring to fig. 9b, CD8 960 may form a dimer comprising a pair of CD8 chains 962, 964 embedded in T cell membrane 950. In various embodiments, CD8 960 comprises CD8- α962 and CD8- β964 chains, thereby forming a heterodimer. In an alternative embodiment, the CD comprises two CD8- α chains, thereby forming a homodimer. In various embodiments, CD8 960 may interact with pMHC. In various embodiments, the CD8- α962 chain of CD8 960 can interact with the α3 globular domain of pMHC. In various embodiments, the assays described herein can characterize CD8: pMHC binding characteristics.
In various embodiments, CD8 chains 962, 964 may be connected by disulfide bonds. In addition, CD8 chains 962, 964 may each include a transmembrane region and a cytoplasmic region. In various embodiments, CD8: the pMHC interaction may be extracellular.
Referring to FIG. 9C, CD4 970 includes four extracellular domains (D 1 972、D2 974、D3 976 and D 4 978).D1 972 and D 3 976 may be variable domains, D 2 974 and D 4 978 may be constant domains in various embodiments, CD4 970 may interact with the β 2 domain of an MHC class II molecule through its D 1 972 domain D 1 972 may include a β -sandwich structure with seven β -strands in 2 β -sheets the cytoplasmic tail 980 of CD4 970 may interact with tyrosine kinase Lck, thereby causing a signaling cascade.
Cell-based ligand-receptor kinetic binding assay
In various embodiments, the compositions detailed herein can be used in ligand-receptor binding assays. For example, a monomeric probe may comprise one or more of the polypeptide molecule fluorophore combinations described herein.
Referring to fig. 3, a cell-based assay for determining association or dissociation rate constants is described. Depicted in fig. 3 shows the overall appearance of the association time point, wherein the signal intensity (e.g., from the detection molecule) increases as more monomer binds to the TCR. It will be clear to those skilled in the art that the appearance of the curvature will vary based on whether the graph depicts association or dissociation. FIG. 4 shows a schematic representation of molecules involved in the binding interaction shown in FIG. 3. In particular, T cells with associated receptors (e.g., TCR, BRC) can bind to monomeric probes.
In various embodiments, the cell-based assay for determining the association rate constant may include lymphocytes (e.g., T cells, B cells) that do not bind to MHC molecules that interact with monomers (e.g., peptide+mhc+ detection molecules) at a given point in time over a period of time. In some embodiments, the time point may begin at 0 minutes and gradually increase until or after MHC molecule binding to the receptor has equilibrated. In some aspects, taking multiple time points between 0 minutes up to equilibrium may increase the accuracy of the assay. The curvature data may be processed to determine an association rate constant representative of living cells.
In various embodiments, cell-based assays for determining dissociation rates are described. Lymphocytes can interact with monomers (e.g., peptide + MHC + detection molecule) until an equilibrium state is reached (e.g., association rate equals dissociation rate). In some embodiments, agents capable of removing monomers from lymphocytes over a period of time may be used. Non-limiting examples of the removing agent may include a dilution buffer, a chemical agent, an environmental condition (e.g., temperature).
In various embodiments, samples may be collected at time points within the time interval. In some embodiments, the point in time may be included between equilibrium (e.g., 0 minutes) and no detectable monomer. In some embodiments, the point in time may be included between an equilibrium (e.g., 0 minutes) and a second equilibrium. In some embodiments, the second equilibrium may include a decrease in the rate of receptor/MHC interactions. In some aspects, taking multiple time points between 0 minutes (e.g., first balance) and up to second balance may increase the accuracy of the assay. The curvature data may be processed to determine an association rate constant representative of living cells.
Monomer probe
Currently, tetramer probes are available for tetramer staining assays. The binding affinity of tetramers to T cells is increased due to their ability to bind to multiple T cell receptors. The increased binding affinity property results in an increased detection capacity. The problem is that allowing the probe to bind multiple TCRs simultaneously means that pMHC is involved: information about TCR living cell binding kinetics (e.g., information about the bimolecular 1TCR 1 pmhc) will be lost.
Aspects of the present disclosure describe monomeric probes suitable for cell-based kinetic assays according to various embodiments. In various embodiments, monomeric probes may be capable of interrogating rate binding properties (e.g., association and dissociation rate constants) by virtue of each probe being capable of binding to only one receptor (e.g., TCR, BCR). The inclusion of a 1:1 (pMHC: receptor) binding ratio allows fluorescence to be compared to many pMHC: receptor binding events correspond. Importantly, the assays described herein using monomeric probes can obtain kon and koff for a two-molecule reaction (1 receptor and 1 ligand (e.g., pMHC molecule)). Thus, the various assays described herein may comprise monomeric probes.
Aspects of the disclosure include embodiments of monomeric probes for use in the various cell-based assays described herein. In addition to the compositions described herein, another non-limiting example of a single probe 402 is depicted in fig. 4. The purpose of the monomer probe 402 may be to mimic an antigen presenting complex (e.g., pMHC) on a cell and bind T cells 412 that are capable of recognizing an antigen (e.g., a peptide).
In various embodiments, the monomeric probes may comprise detection molecules 408 attached to MHC molecules 404.
In various embodiments, MHC molecules 404 may comprise MHC class I molecules. In various embodiments, MHC molecules 404 may comprise MHC class II molecules. In various embodiments, MHC molecule 404 may bind peptide 410. In various embodiments, the nature of the peptide may help determine the binding kinetics between MHC molecule 404 and receptor molecule 414. In some embodiments, the binding kinetics of MHC molecules 404 and receptor molecules 414 can determine whether T cells 412 are activated and result in cell death of cells that may be associated with MHC molecules 404.
In various embodiments, MHC molecule 404 may be linked to detection molecule 408 through linker 406. In various embodiments, the linker 406 can include a lysine residue, and the detection molecule 408 can comprise a fluorophore that binds to the lysine residue, as described herein (including the examples section).
In some embodiments, the coupling may be direct or through intermediaries. In various embodiments, the detection molecule 408 may comprise avidin or streptavidin, and the MHC molecule 404 may comprise biotin. In various embodiments, the detection molecule 408 may comprise biotin and the MHC molecule 404 may comprise avidin or streptavidin. In some aspects, binding of biotin to streptavidin results in the formation of monomeric probe 402. In the above sections, biotin and (streptavidin or avidin) may comprise a linker 406. In some embodiments, the linker 406 may comprise a single molecule. In other embodiments, the linker 406 may comprise more than one molecule (e.g., biotin and (streptavidin or avidin)).
Non-limiting examples of detection molecules 408 may include fluorophores, quencher forster resonance energy transfer systems (e.g., FRET), or other molecules that may be quantitatively interrogated.
In various embodiments, a composition for use in a biological kinetic assay may comprise: a polypeptide molecule comprising an antigen binding region; one or more fluorophores linked to the polypeptide molecule; and an antigenic peptide that binds to the antigen binding region of the polypeptide molecule.
In various embodiments, a composition for use in a biological kinetic assay may comprise: a polypeptide molecule comprising an antigen binding region; one or more fluorophores linked to the polypeptide molecule; and an antigenic peptide that binds to the antigen binding region of the polypeptide molecule, wherein the antigenic peptide comprises UV cleavable amino acids.
In some embodiments, the polypeptide molecule comprises a single polypeptide chain. In other embodiments, the polypeptide molecule may comprise a first polypeptide chain and a second polypeptide chain.
In various embodiments, the antigen binding region of the polypeptide molecule can comprise at least a portion of a first polypeptide chain of the polypeptide molecule.
In some embodiments, the first polypeptide chain can comprise an α 1 domain and an α 2 domain. In some embodiments, the first polypeptide chain can comprise an α 3 domain.
In various embodiments, the first polypeptide chain may comprise an amino acid sequence of a recombinant human leukocyte antigen.
In various embodiments, the first polypeptide chain can comprise the amino acid sequence of recombinant murine histocompatibility system 2.
In various embodiments, the second polypeptide chain can be linked to the α 3 domain of the first polypeptide chain.
In various embodiments, the second polypeptide chain comprises the amino acid sequence of a β 2 -microglobulin molecule.
In various embodiments, the antigen binding region comprises at least a portion of a first polypeptide chain and at least a portion of a second polypeptide chain.
In various embodiments, a portion of the first polypeptide chain comprises an α 1 domain, a portion of the second polypeptide chain comprises a β 1 domain, and the α 1 domain and the β 1 domain form an antigen binding region. In some embodiments, the first polypeptide chain further comprises an α 2 domain. In some embodiments, the second polypeptide chain further comprises a β 2 domain. In many embodiments, the first polypeptide chain comprises an amino acid sequence of a recombinant human leukocyte antigen. In many embodiments, the second polypeptide chain comprises a polypeptide sequence of a recombinant human leukocyte antigen.
In various embodiments, the antigen binding region comprises at least one alpha-helix. In some embodiments, the antigen binding region comprises at least one β -sheet.
In various embodiments, one or more fluorophores are covalently linked to the polypeptide molecule. In some embodiments, the covalent bonding comprises an ester. In various embodiments, one or more fluorophores are covalently linked to one or more solvent-exposed surface lysine residues of the polypeptide molecule.
In various embodiments, the first polypeptide chain and the second polypeptide chain are non-covalently linked. In alternative embodiments, the first polypeptide chain and the second polypeptide chain are covalently linked.
In various embodiments, the polypeptide molecule may bind to an antigen presenting cell surrogate. In various embodiments, the antigen presenting cell replacement comprises a bead. In various embodiments, the polypeptide molecule is attached to the antigen presenting cell replacement via a linker. In some embodiments, the linker comprises a polyethylene glycol (PEG) molecule.
In many embodiments, the composition further comprises a receptor that binds to an antigen binding region of the polypeptide molecule.
In various embodiments, a composition comprises living lymphocytes. In some embodiments, at least a portion of the receptor is located on the cell membrane of a living lymphocyte. In some embodiments, the co-receptor may be located on the cell membrane of a living lymphocyte. In some embodiments, the co-receptor binds to a portion of the polypeptide molecule. In various embodiments, the living lymphocyte is a T cell and the receptor is a T Cell Receptor (TCR). In various embodiments, the co-receptor comprises a CD8 molecule. In other embodiments, the living lymphocyte is a B cell and the receptor is a B Cell Receptor (BCR). In some embodiments, the co-receptor comprises a CD4 molecule. In still other embodiments, the living cells comprise macrophages and the receptors comprise chemokine receptors. In still other embodiments, the living cells comprise dendritic cells and the receptor comprises a Pattern Recognition Receptor (PRR).
In various embodiments of the assay, naturally occurring peptide 410 may be interrogated. In some embodiments, the artificially generated (e.g., synthetic, expression vector, etc.) peptide 410 may be interrogated. The skilled artisan will appreciate that the embodiments herein may benefit from existing peptide libraries. Additional embodiments may include the manufacture of peptide libraries.
Aspects of the described systems and methods may relate to assaying a variety of different receptors. In various embodiments, peptides may be selected based on the particular receptor determined. For example, several peptides are known to bind to OT-1 TCR with different intensities. Thus, in some embodiments, known peptide sequences may be determined.
In various embodiments, the peptides produced may be assayed. Non-limiting examples of methods for manufacturing peptides may include Solid Phase Peptide Synthesis (SPPS). In some embodiments, the SPPS can assemble peptide chains by sequential reaction of the amino acid derivative on a support (e.g., an insoluble porous support).
In some embodiments, peptides 410 with characterized binding properties may be deployed for characterization-based therapies. In other embodiments, research and development may benefit from being able to deploy peptides 410 with characterized binding properties.
In various embodiments, the antigenic peptide ranges from 8 to 11 amino acid residues in length. In other embodiments, the antigenic peptide ranges from 15 to 24 residues in length. In some embodiments, the antigenic peptide comprises a UV moiety.
Reaction mixture
The present invention provides reaction mixtures for generating probe complexes for use in a biological kinetic assay. In various embodiments, the reaction mixture can comprise one or more of the compositions described herein and a target antigen peptide. In various reactions, the target antigenic peptide may be present in a molar excess compared to the antigenic peptide bound to the antigen binding region of the polypeptide molecule. In the various reaction mixtures, the concentration of the target antigen peptide was 25 times the concentration of the antigen peptide. The various reaction mixtures may comprise 25mM TRIS. The various reaction mixtures may comprise a pH of 8.0. The various reaction mixtures may contain 150mM NaCl. The various reaction mixtures may comprise 4mM EDTA. The various reaction mixtures may comprise 5% ethylene glycol.
Instrument system
Aspects of the present disclosure may benefit from an instrument system for collecting quantitative data. In various embodiments, the analyte (e.g., ligand-receptor) may be labeled with a detection molecule that is detectable by the instrument system. In various embodiments, the instrumentation system may comprise a detection system. In various embodiments, the instrument system may include optical system components. In various embodiments, the instrument system may include fluid system components. In various embodiments, the instrument system may include control system components.
The methods described herein can be implemented on any instrument system capable of quantifying the binding kinetics between a ligand and a receptor (e.g., measuring the signal intensity from a detection molecule). Some embodiments benefit from a high throughput system including flow cytometry.
Flow cytometry is designed to analyze large numbers of cells by passing the cells through a detection zone at a very high rate. In the accompanying method, a population of cells may be prepared for interrogation at different points along a time interval to generate an association or dissociation curve. In order to accurately characterize the rate constants contributing to the curve, a large amount of binding kinetics data may be required. Thus, monomeric probes (e.g., pMHC and associated detection molecules) that bind to TCRs of T cells can be well suited for flow cytometry analysis.
FIG. 14 is a schematic diagram of a system for measuring binding kinetics to assess living cell activation, in accordance with various embodiments. In various embodiments, the system comprises an analysis device 1400 comprising an analysis chamber 1404, wherein the analysis chamber 1404 comprises a composition described herein. The present invention provides a system for measuring binding kinetics to assess living cell activation comprising an analytical device 1400 comprising an analytical chamber 1404, wherein the analytical chamber 1404 comprises a reaction mixture as described herein. In various systems, the analysis device 1400 includes a light source 1402 for interrogating an analysis chamber 1404 and a detector 1406 for detecting a signal.
In various embodiments, computer system 1408 comprises a non-transitory computer-readable storage medium, wherein the non-transitory computer-readable storage medium comprises instructions for analyzing the signal.
In various embodiments, analyzing the signal includes normalizing the signal with respect to a previously determined calibration value.
In various embodiments, analysis chamber 1404 includes a flow cell.
In various embodiments, the analysis device 1400 comprises a flow cytometer. In various embodiments, the analysis device 1400 comprises a fluorometer. In various embodiments, the analysis device 1400 comprises a microscope. In various embodiments, the analysis device 1400 comprises a mass spectrometer.
Method-formation of monomeric probe complexes
The present invention provides methods of forming monomeric probe complexes. Various methods include contacting a polypeptide molecule comprising an antigen binding region with a first antigen peptide to generate an antigen presenting complex, contacting the antigen presenting complex with a plurality of fluorophore molecules to generate a fluorophore-labeled antigen presenting complex, determining the concentration of fluorophore molecules covalently bound to the fluorophore-labeled antigen presenting complex, and exchanging the first antigen peptide with a second antigen peptide to generate a monomeric probe complex.
In various embodiments, a method of generating a monomeric probe complex includes the step of exchanging a first antigenic peptide with a second antigenic peptide, the step including cleaving the first antigenic peptide to generate a cleaved first antigenic peptide.
In various embodiments, a method of generating a monomeric probe complex includes a step of cleaving a first antigenic peptide, the step including applying UV radiation.
In various methods, the second antigenic peptide has a higher affinity for the antigen binding region than the cleaved first antigenic peptide.
In various methods, the UV radiation comprises a wavelength of 365 nm.
In various embodiments, a method of generating a monomeric probe complex includes the step of contacting an antigen presenting complex with a plurality of fluorophore molecules to generate fluorophore-labeled antigen presenting complexes, the step including covalently linking one or more solvent-exposed surface lysine residues of a polypeptide molecule to one or more of the fluorophore molecules.
In various embodiments, a method of generating a monomeric probe complex includes the step of separating one or more unconjugated fluorophores from a labeled monomeric probe complex.
In various embodiments, a method of generating a monomeric probe complex includes determining a concentration of a plurality of labeled monomeric probe complexes.
In various embodiments, a method of generating a monomeric probe complex includes determining an average number of fluorophores conjugated to each of a plurality of labeled monomeric probe complexes. In some embodiments, the step of determining an average number of fluorophores conjugated to each of the plurality of labeled monomeric probe complexes comprises using a plurality of relative abundance values, wherein each relative abundance value corresponds to a different number of conjugated fluorophores. In some embodiments, each of the plurality of relative abundance values is determined using mass spectrometry.
Method-association
Fig. 5A is a flow chart of a process 550 for collecting association rate data to assess living cell activation, in accordance with various embodiments.
Step 552 includes contacting a plurality of living cells with a plurality of compositions at a concentration, wherein each of the plurality of living cells comprises a plurality of receptor molecules on a cell membrane. In various embodiments, the living cells comprise T cells. In various embodiments, the living cells comprise B cells. In various embodiments, the living cells comprise macrophages. In various embodiments, the living cells comprise dendritic cells.
Step 554 includes binding a receptor molecule to the composition over a time interval to form a plurality of receptor-probe complexes, wherein each receptor-probe complex comprises a composition that binds to a receptor. In some embodiments, each of the receptor-probe complexes comprises a CD8 molecule. In some embodiments, each of the receptor-probe complexes comprises a CD4 molecule.
Step 556 includes collecting at least two samples of the plurality of living cells at different points in time within the time interval.
Step 558 includes contacting living cells in each of the at least two samples with an immobilization agent to preserve the receptor-probe complex and prevent further binding between the receptor molecule and the composition. In various embodiments, the fixing agent comprises paraformaldehyde.
Step 560 includes determining the number of receptor-probe complexes on the cell membrane of each cell.
Step 562 includes analyzing the number of receptor-probe complexes on the cell membrane of each cell in each sample to collect association rate data.
In various embodiments, the signal strength of the composition is measured using an analytical device. In various embodiments, the analysis device comprises a flow cytometer. In some embodiments, the analysis device comprises a fluorometer.
In various embodiments, the method may include preventing receptor internalization by reducing the temperature of the receptor-probe complex. In many embodiments, the temperature is reduced to 4 ℃.
In various embodiments, the method can include isolating one or more unbound compositions from the plurality of living cells.
Fig. 5B is a flow chart of a process 500 for collecting biophysical parameter data to assess the rate of association of a T Cell Receptor (TCR) with a peptide-major histocompatibility complex (pMHC), according to some embodiments.
In various embodiments, the TCR molecule can be expressed on a T cell. For non-limiting examples, the TCR molecule can be located in, at, or near the cell membrane of a T cell.
Step 502 includes generating a set of monomeric probes, wherein each monomeric probe comprises a detection molecule and one MHC comprising a peptide.
Step 504 includes associating TCR molecules with monomeric probes in a one-to-one correspondence to form TCR-monomeric probe complexes over a time interval. In some embodiments, the time interval may begin prior to the equilibrium state of the TCR-monomer probe complex.
Step 506 includes sampling two or more subsets of TCR-monomer probe complexes over the time interval, wherein each subset is acquired at a different point in time.
Step 508 includes preventing the formation of new TCR-monomer probe complexes within each subgroup at their corresponding time points. In some aspects, the preventing step may include using a fixing buffer. According to some embodiments, the immobilization buffer may prevent the reaction from proceeding forward. In some embodiments, a PBS solution of 4% pfa may be used as the fixation buffer. In some cases, embodiments may include reducing the temperature after the preventing step. This step of addition in the protocol may further prevent formation and may be used to preserve the sample. In some embodiments, the temperature may be 4 degrees celsius.
Step 510 includes measuring the signal intensity from the detection molecules in each subset using an analytical device.
In various embodiments, the detection molecule comprises a fluorescent molecule. In some embodiments, the detection molecule may comprise a quencher. In various embodiments, the detection molecule and MHC may be coupled by a linker. In some embodiments, the linker comprises a biotinylated structure. In some embodiments, the linker may comprise one, two, three, four, five, six, or any number of molecules. Non-limiting examples of a polymolecular linker include biotin bound to avidin or streptavidin. In alternative embodiments, the linker comprises PEG.
In various embodiments, the analysis device comprises a flow cytometer. In some embodiments, analytical properties of the flow cytometer may be suitably applied. Non-limiting examples of analytical properties may include high throughput capability by running carrier fluid cells through a flow cell at high rates.
In various embodiments, the method may further comprise the step of isolating unbound monomeric probes from the TCR molecules. Non-limiting examples may include one or more washing steps.
Method-dissociation
FIG. 6A is a flowchart of a process 650 for collecting dissociation rate data to assess living cell activation, according to various embodiments.
Step 652 comprises contacting a plurality of living cells with a plurality of compositions at a concentration, wherein each of the plurality of living cells comprises a plurality of receptor molecules on a cell membrane. In various embodiments, the living cells comprise T cells. In various embodiments, the living cells comprise B cells. In various embodiments, the living cells comprise macrophages. In various embodiments, the living cells comprise dendritic cells.
Step 654 includes binding the receptor molecules to the composition to form a plurality of receptor-probe complexes until equilibrium is reached, wherein each receptor-probe complex comprises a composition that binds to a receptor. In some embodiments, each of the receptor-probe complexes comprises a CD8 molecule. In some embodiments, each of the receptor-probe complexes comprises a CD4 molecule.
Step 656 includes dissociating a portion of the receptor-probe complex over a time interval by reducing the concentration of the composition.
Step 658 includes collecting at least two samples of the plurality of living cells at different points in time within the time interval.
Step 660 includes contacting the living cells in each of the at least two samples with an immobilization agent to preserve the receptor-probe complex and prevent further binding between the receptor molecules and the composition. In various embodiments, the fixing agent comprises paraformaldehyde.
Step 662 includes determining the number of receptor-probe complexes on the cell membrane of each cell.
Step 664 includes analyzing the number of receptor-probe complexes on the cell membrane of each cell in each sample to collect association rate data.
In various embodiments, the signal strength of the composition is measured using an analytical device. In various embodiments, the analysis device comprises a flow cytometer. In some embodiments, the analysis device comprises a fluorometer.
In various embodiments, the method may include preventing receptor internalization by reducing the temperature of the receptor-probe complex. In many embodiments, the temperature is reduced to 4 ℃.
In various embodiments, the method can include isolating one or more unbound compositions from the plurality of living cells.
Referring to fig. 6B, a method for collecting biophysical parameter data to assess the rate of dissociation of T Cell Receptor (TCR) from peptide-major histocompatibility complex (pMHC) is depicted according to some embodiments. In various embodiments, the TCR molecule can be expressed on a T cell.
Step 602 includes generating a set of monomeric probes. Exemplary embodiments of various monomeric probes are described in the "monomeric probe" section. In some embodiments, each monomeric probe comprises a detection molecule and one MHC comprising a peptide. In various embodiments, the detection molecule may comprise a fluorescent molecule. In some embodiments, the detection molecule and MHC may be coupled by a linker. Non-limiting examples of linkers can include biotinylated structures including biotin, avidin, and streptavidin. In alternative examples, the linker may comprise PEG.
Step 604 includes associating TCR molecules with monomeric probes in a one-to-one correspondence to form TCR-monomeric probe complexes. In some embodiments, the TCR molecule can comprise a T cell receptor molecule.
Step 606 includes dissociating the TCR-monomer probe complex into a monomer probe and a TCR over a time interval. In various embodiments, the time interval may begin at the equilibrium state of the TCR-monomer probe complex. In some embodiments, TCR molecules and monomeric probes may be pre-incubated to reach an equilibrium state. The method may further comprise diluting the solution comprising the TCR-monomer probe complex with a buffer, thereby causing dissociation. In some embodiments, the buffer may comprise a dilution buffer.
Step 608 includes sampling two or more subsets of TCR-monomer probe complexes over the time interval, wherein each subset is acquired at a different point in time.
Step 610 includes preventing dissociation of additional TCR-monomer probe complexes within each subset at their corresponding time points. In some aspects, the preventing step may include using a fixing buffer. In some embodiments, the method may further comprise the step of reducing the temperature after the preventing step. Non-limiting examples of temperatures include 4 degrees celsius.
Step 612 includes measuring the signal intensity from the detection molecules in each subset using a high throughput analysis device. In various embodiments, the analysis device may comprise a flow cytometer.
Embodiments of the method may include the additional step of separating unbound monomeric probes from TCR molecules. In some embodiments, the separating may include washing.
Examples
Example 1: components of probe complexes
Recombinant human β 2 -microglobulin (B2M). B2M binds to Human Leukocyte Antigen (HLA) or murine histocompatibility system 2, forming a non-covalent complex through interaction with the α 3 domain. The resulting heterodimer is the Major Histocompatibility Complex (MHC) class I. With sufficient sequence homology, human B2M can be used for human and mouse MHC.
Recombinant Human Leukocyte Antigen (HLA) or recombinant murine histocompatibility System 2 (H-2) (the alpha chain of MHC class I complex). When complexed with β 2 -microglobulin, the α 1 and α 2 domains form a peptide binding groove capable of non-covalent binding of specific peptides of 8 to 11 amino acids in length.
A peptide. The synthetic 8-11 polypeptide is derived from human, murine, chicken or viral proteins. These peptides bind with nanomolar to micromolar affinity to the peptide binding groove of the a 1 and a 2 domains of HLA complexed with β 2 -microglobulin. Peptide binding to MHC class I stabilizes the recombinant non-covalent complex. The epitope peptide binds to MHC class I to form an antigen recognized by the T Cell Receptor (TCR).
N-hydroxysuccinimide (NHS) -ester fluorophore. When added in molar excess under optimal reaction conditions, the NHS-ester fluorophore (Alexa Fluor TM 488 NHS Ester) was covalently conjugated to solvent-exposed surface lysine residues of MHC class I. Fluorescence measurements can be performed on probes bound to the TCR. The NHS-ester fluorophore is selected based on UV resistance.
Example 2: initial component of probe synthesis method
UV-MHC class I or peptide-MHC class I. Refolding of recombinant MHC class I is performed with high affinity 8-11 oligopeptides (including unnatural, UV cleavable amino acids) or with epitope peptides of interest. Peptides are commercially available or produced internally. Peptides, e.g., grotenbreg, gijsbert m et al, "cd8+ T cell epitope (Discovery of CD8+ T cell epitopes in Chlamydia trachomatis infection through use of caged class I MHC tetramers)"PNAS,2008., volume 105, phase 10, pages 3831-3838, found in chlamydia trachomatis infection by use of a caged MHC class I tetramer," the disclosure of which is incorporated herein by reference in its entirety. This process is shown in fig. 12.
For the UV-MHC class I complex, the UV cleavable peptide is a conditional ligand that allows for the exchange of the epitope peptide of interest into the peptide binding groove of the complex. This process is shown in fig. 13.
UV-MHC or peptide-MHC class I molecules are labeled with fluorophores. The UV-MHC class I molecules are then loaded with the peptide of interest by UV-mediated exchange to form the final probe.
A peptide. Lyophilized synthetic peptides of length 8 to 11 amino acids with a purity > 90% were used. The peptide of interest is added in molar excess to a specific UV-MHC for UV-mediated exchange into the complex (see fig. 13), or for direct generation of peptide-MHC class I molecules by refolding with B2M and HLA.
NHS-ester fluorophores. NHS-ester fluorophores are added in molar excess to UV-MHC class I molecules or peptide-MHC class I molecules to conjugate with surface exposed lysine residues. The fluorophore chosen must be able to withstand downstream exposure to 365nm UV light. An example of a fluorophore used is Alexa Fluor TM 488.
Example 3: method for synthesizing probe
UV-MHC was labeled with a fluorophore. The desired allele of UV-MHC was incubated with a 2-20 molar excess of NHS-fluorophore in phosphate buffered saline pH 7.4 for 2 hours at room temperature. Excess unconjugated fluorophore was removed by dialysis. Samples were loaded into a 10K cutoff molecular weight dialysis cartridge (Slide-A-Lyzer TM K MWCO cartridge, thermo Fisher TM) and placed in 25mM TRIS pH 8.0, 150mM NaCl, 4mM EDA, samples: the ratio of the dialyzate is 1:2000. The sample and dialysate were incubated at 4 ℃ for 8 hours while continuously mixing using a magnetic stir plate. The dialysate was then discarded, replaced with dialysate, and incubated at 4 ℃ for an additional 8 hours while stirring. After the second round of dialysis, the samples were recovered, the protein concentration was determined using a UV-visible spectrophotometer, and the contribution of the fluorophore to absorbance at 280nm was corrected.
The extent of fluorophore labelling was determined. The extent of fluorophore labelling was determined by reverse phase liquid chromatography mass spectrometry (RP LC-MS). 2-3 μg MHC-fluorophore conjugation reactions were injected into Agilent TM 1290 InfinityTM series HPLC equipped with an Agilent 6230 TM time-of-flight electrospray ionization mass spectrometer. Injecting the sample into a reversed phase chromatographic column (Agilent TM PLRP-S)8 Μm,50×2.1 mm). The column was exposed to a gradient of 25% to 45% mobile phase B at a rate of 0.50 mL/min over 5min and heated to 80 ℃. Mobile phase a was 0.05% tfa. Mobile phase B was 0.05% tfa in acetonitrile. The chromatographic column eluent is sent to LC-MS for mass spectrum data acquisition. The extent of fluorophore conjugation can be determined by deconvolution mass spectrometry using peaks corresponding to B2M and HLA. The average number of fluorophores per pMHC class I molecule is calculated by using the relative abundance of each mass corresponding to the number of different fluorophores added to each protein class and determining a weighted average of the complexes.
UV-mediated peptide exchange. Peptides were dissolved in ethylene glycol to a concentration of 20mg/mL and added to the fluorophore-labeled peptide-MHC I molecules in 25-fold molar excess. The peptide exchange reaction was performed in 25mM TRIS pH 8.0, 150mM NaCl, 4mM EDTA, and contained 5% ethylene glycol v/v after the peptide addition. The final concentration of peptide-MHC I molecules in the exchange reaction was 2.0mg/mL. The peptide exchange reaction was performed in UV transparent 96 well plates or transparent colorless sample tubes, up to 15mL in volume.
The peptide exchange reaction was then incubated under UV light (Analytikjena TM UVP 3UV lamp) set at 365nm for 20 minutes. The lamp is placed as close as possible to the sample container. After exposure to UV light, the exchange reaction was allowed to proceed at room temperature for a minimum or 4 hours, or incubated overnight.
Determination of peptide binding to MHC. Two-dimensional liquid chromatography mass spectrometry (2D LC-MS) methods were used to characterize peptide binding to MHC class I complexes. 2-3 μg of the MHC class I peptide mixture was injected onto the instrument and sent to the first dimension column. The first dimension LC method employs analytical Size Exclusion Column (SEC) (Agilent TM AdvanceBioTM SEC)2.7Um, 4.6x15mm) from excess peptide, run in 25mM TRIS pH 8.0, 150mM NaCl at an isocratic flow rate of 0.7 ml/min for 10 min, and collect signal at 280 nm. The sampling valve collects all complex peaks eluting in a volume of 160 μl between 1.90 and 2.13 minutes and injects them into a second dimension reverse phase chromatography column (Agilent) TM PLRP-STM 8Um,50x2.1 mm). The second dimension column was exposed to a gradient of 5% to 50% mobile phase B at a rate of 0.55 ml/min over 4.7 min and the column was heated to 80 ℃. Mobile phase a was 0.05% tfa. Mobile phase B was 0.05% tfa in acetonitrile. The column eluate was sent to Agilent 6224 TOF LCMS for mass spectrometry data acquisition.
Example 4: pMHC-OVA association assay
In the TCR association assay, OT-I cells are used, which are derived from a murine transgenic line that produces MHC class I restricted, ovalbumin specific CD8+ T cells (OT-I cells). OT-I cells have T cell antigen receptors consisting of the alpha-chain variable region 2 (V.alpha.2) and the beta-chain variable region 5 (V.beta.5), which are inherited by a single transgene.
OT-I cells were first counted for 82% viability with some dead cell debris. OT-I cells were resuspended 400 ten thousand per mL in buffer (e.g., 1 XPBS, 0.5% BSA+2mM EDTA or 1 XPBS, 0.5% BSA+0.05% sodium azide) and stained with anti-TCRβ (H57-597 1/600) and reactive dye (1/1000). Then 100. Mu.L of OT-I cells were dispensed into each well of a 96-well plate. The OT-I cells were then washed by adding 150. Mu.L of 1 XPBS, 0.5% BSA+0.05% sodium azide buffer and centrifuging at 1400rpm for 2.5 minutes. The calibration beads were also stained as a method of measuring the number of cell surface receptors.
Solutions comprising monomeric probe complexes with ligand peptides and IgG antibodies were prepared as follows:
N4 monomer 100. Mu.g/mL = 30. Mu.L 2mg/mL monomer + 570. Mu.L 1 XPBS, 0.5% BSA +0.05% sodium azide buffer
N4 monomer 50 μg/mL = 15 μl 2mg/mL monomer +585 μl1 XPBS, 0.5% BSA +0.05% sodium azide buffer
N4 monomer 20 μg/mL = 6 μl 2mg/mL monomer +594 μl 1 XPBS, 0.5% BSA +0.05% sodium azide buffer
T4 monomer 100 μg/mL = 30 μl 2mg/mL monomer +570 μl 1x PBS, 0.5% bsa +0.05% sodium azide buffer
T4 monomer 50 μg/mL = 15 μl 2mg/mL monomer +585 μl1x PBS, 0.5% bsa +0.05% sodium azide buffer
T4 monomer 20 μg/mL = 6 μl 2mg/mL monomer +594 μl 1x PBS, 0.5% bsa +0.05% sodium azide buffer
V4 monomer 100 μg/mL = 30 μl 2mg/mL monomer +570 μl 1x PBS, 0.5% bsa +0.05% sodium azide buffer
V4 monomer 50 μg/mL = 15 μl 2mg/mL monomer +585 μl1x PBS, 0.5% bsa +0.05% sodium azide buffer
V4 monomer 20 μg/mL = 6 μl 2mg/mL monomer +594 μl 1x PBS, 0.5% bsa +0.05% sodium azide buffer
Igg antibody (for stained beads) 100 μg/mL = 33 μl 1.8mg/mL +557 μl 1x PBS, 0.5% bsa +0.05% sodium azide buffer
11. Peptide 100 μg/mL = 14.3 μl 4.2mg/mL +586 μl 1x PBS, 0.5% bsa +0.05% sodium azide buffer only
120. Mu.L of the solution containing the monomer, peptide and antibody was added to a 96-well plate (immobilization plate for reagents before transfer). 100. Mu.L of each solution was transferred into cells using a multichannel pipette. Cells were stained at time points 0, 3,9, 27 and 81 minutes. At each time point, 150 μl Cytofix TM buffer was added to the wells to stop the reaction and the cells were transferred to another plate. The cells were then incubated at 4 degrees for 20 to 40 minutes. After the fixation at each time point was completed, the cells were centrifuged for 2.5 minutes using a centrifuge operating at 1500rpm, and then 200 μl of 1x PBS, 0.5% bsa+0.05% sodium azide buffer was added. All cells were pooled into one plate and stained using the same template for running in a flow cytometer. The cells were centrifuged for 2.5 minutes using a centrifuge operating at 1500rpm, and then 130 μl of buffer was added. 100. Mu.L of the cell-containing solution was run on 1 XPBS, 0.5% BSA+0.05% sodium azide at a rate of 0.5. Mu.L per second (1. Mu.L per second may be used). Example data for collecting data and N4 are illustrated in fig. 7A and 7B.
To detect the phosphorylation level of the zeta domain of the TCR, cells were washed with 1x permeabilization buffer (Thermo FISHER SCIENTIFIC TM 00-8333-56) and then incubated with anti-pCD 247 CD3 zeta Tyr142 APC (Thermo FISHER SCIENTIFIC TM 17-2478-42) diluted 1:50 in 1x permeabilization buffer for 30 min at room temperature. The cells are then washed with 1x permeabilization buffer and resuspended in buffer (e.g., 1x PBS, 0.5% bsa+2mm EDTA or 1x PBS, 0.5% bsa+0.05% sodium azide) for subsequent flow cytometry analysis.
Example 5: pMHC-OVA dissociation assay
In the TCR dissociation assay, OT-I cells were first counted for 50% viability. Dead cells were removed using a dead cell removal kit. Cells were then counted again with a viability of 75%.
400K cells were then deposited into each well of a 96-well plate (not all wells were used). Cells were centrifuged using a centrifuge and stained with anti-TCR beta (H57-597 1/600) and vital dye (1/1000) in 1 XPBS, 100. Mu.L of 0.5% BSA+0.05% sodium azide buffer was added to each well. Cells were incubated at room temperature for 20 min, then 150 μl of 1 xpbs, 0.5% bsa+0.05% sodium azide buffer was added, and the cells were centrifuged using a centrifuge.
Solutions comprising monomeric probe complexes with ligand peptides and IgG antibodies were prepared as follows:
N4 monomer 100. Mu.g/mL = 30. Mu.L 2mg/mL monomer + 570. Mu.L 1 XPBS, 0.5% BSA +0.05% sodium azide buffer
T4 monomer 100. Mu.g/mL = 30. Mu.L 2mg/mL monomer + 570. Mu.L 1 XPBS, 0.5% BSA +0.05% sodium azide buffer
3.V4 monomer 100 μg/mL = 30 μl 2mg/mL monomer +570 μl 1x PBS, 0.5% bsa +0.05% sodium azide buffer
Igg antibody (for beads) 100 μg/mL = 33 μl 1.8mg/mL +557 μl 1x PBS, 0.5% bsa +0.05% sodium azide buffer
5. Peptide 100 μg/mL = 14.3 μl 4.2mg/mL +586 μl 1x PBS, 0.5% bsa +0.05% sodium azide buffer only
100. Mu.L of the sample was then transferred to the plate containing the cells using a multichannel pipette to minimize time differences. The cells were then incubated for one hour at room temperature. The samples were covered with buffer and centrifuged with a centrifuge. Two additional washes were performed using 200 μl 1x PBS, 0.5% bsa+0.05% sodium azide buffer.
Samples were then incubated at room temperature at time points 0, 3, 9, 27 and 81 minutes. At these time points, 300 μl Cytofix TM buffer was added and mixed with each sample. The samples were then transferred to fresh plates and fixed for 20 to 40 minutes, centrifuged using a centrifuge, and resuspended in (e.g., 1 XPBS, 0.5% BSA+2mM EDTA or 1 XPBS, 0.5% BSA+0.05% sodium azide) buffer.
To detect the phosphorylation level of the zeta domain of the TCR, the cells were washed with 1x penetration buffer (Thermo FISHER SCIENTIFIC TM 00-8333-56) and then incubated with anti-pCD 247 CD3 zeta Tyr142 APC (Thermo FISHER SCIENTIFIC TM 17-2478-42) diluted 1:50 in 1x penetration buffer for 30 min at room temperature. The cells are then washed with 1x permeabilization buffer and resuspended in (e.g., 1x PBS, 0.5% bsa+2mm EDTA or 1x PBS, 0.5% bsa+0.05% sodium azide) buffer for subsequent flow cytometry analysis.
The cells were then centrifuged using a centrifuge and resuspended in 130 μl 1 xPBS, 0.5% BSA+0.05% sodium azide buffer. The samples were then run on a BD Symphony TM using a plate reader at a rate of 0.5 μl per second. Example data for collecting data and N4 are illustrated in fig. 8A and 8B.
While the present teachings are described in connection with various embodiments, the present teachings are not intended to be limited to such embodiments. On the contrary, the present teachings encompass various alternatives, modifications, and equivalents as will be appreciated by those of skill in the art.
In describing various embodiments, the specification may have presented the method and/or process as a particular sequence of steps. However, to the extent that the method or process does not rely on the particular order of steps set forth herein, the method or process should not be limited to the particular sequence of steps described, and those skilled in the art will readily appreciate that the sequences may be varied and still remain within the spirit and scope of the various embodiments.
Claims (115)
1. A composition for use in a biological kinetic assay, the composition comprising:
a polypeptide molecule comprising an antigen binding region;
one or more fluorophores linked to the polypeptide molecule; and
An antigenic peptide that binds to said antigen binding region of said polypeptide molecule.
2. A composition for use in a biological kinetic assay, the composition comprising:
a polypeptide molecule comprising an antigen binding region;
one or more fluorophores linked to the polypeptide molecule; and
An antigenic peptide that binds to the antigen binding region of the polypeptide molecule, wherein the antigenic peptide comprises UV cleavable amino acids.
3. The composition of any one of the preceding claims, wherein the polypeptide molecule comprises a single polypeptide chain.
4. The composition of claim 3, wherein the polypeptide molecule comprises a first polypeptide chain and a second polypeptide chain.
5. The composition of claim 4, wherein the antigen binding region comprises at least a portion of the first polypeptide chain of the polypeptide molecule.
6. The composition of claim 5, wherein the first polypeptide chain comprises an a 1 domain and an a 2 domain.
7. The composition of claim 6, wherein the first polypeptide chain comprises an a 3 domain.
8. The composition of any one of claims 3 to 7, wherein the first polypeptide chain comprises an amino acid sequence of a recombinant human leukocyte antigen.
9. The composition of any one of claims 3 to 7, wherein the first polypeptide chain comprises the amino acid sequence of recombinant murine histocompatibility system 2.
10. The composition of any one of claims 6 to 9, wherein the second polypeptide chain is linked to the a 3 domain of the first polypeptide chain.
11. The composition of any one of claims 3 to 10, wherein the second polypeptide chain comprises the amino acid sequence of a β 2 -microglobulin molecule.
12. The composition of claim 3, wherein the antigen binding region comprises at least a portion of the first polypeptide chain and at least a portion of the second polypeptide chain.
13. The composition of claim 12, wherein the portion of the first polypeptide chain comprises an a 1 domain, the portion of the second polypeptide chain comprises a β 1 domain, and the a 1 domain and the β 1 domain form the antigen binding region.
14. The composition of claim 13, wherein the first polypeptide chain further comprises an a 2 domain.
15. The composition of claim 13, wherein the second polypeptide chain further comprises a β 2 domain.
16. The composition of any one of claims 12 to 15, wherein the first polypeptide chain comprises an amino acid sequence of a recombinant human leukocyte antigen.
17. The composition of any one of claims 12 to 16, wherein the second polypeptide chain comprises a polypeptide sequence of a recombinant human leukocyte antigen.
18. The composition of claim 17, wherein the antigen binding region comprises at least one a-helix.
19. The composition of any one of claims 17 to 18, wherein the antigen binding region comprises at least one β -sheet.
20. The composition of any one of the preceding claims, wherein the one or more fluorophores are covalently linked to the polypeptide molecule.
21. The composition of claim 20, wherein covalent bonding comprises an ester.
22. The composition of any one of the preceding claims, wherein the one or more fluorophores are covalently linked to one or more solvent exposed surface lysine residues of the polypeptide molecule.
23. The composition of any one of claims 3 to 22, wherein the first polypeptide chain and the second polypeptide chain are non-covalently linked.
24. The composition of any one of claims 3 to 22, wherein the first polypeptide chain and the second polypeptide chain are covalently linked.
25. The composition of any one of the preceding claims, wherein the polypeptide molecule binds to an antigen presenting cell surrogate.
26. The composition of claim 25, wherein the antigen presenting cell replacement comprises a bead.
27. The composition of any one of claims 25 to 26, wherein the polypeptide molecule is attached to the antigen presenting cell substitute by a linker.
28. The composition of claim 27, wherein the linker comprises a polyethylene glycol (PEG) molecule.
29. The composition of any one of the preceding claims, further comprising a receptor that binds to the antigen binding region of the polypeptide molecule.
30. The composition of claim 29, further comprising a living lymphocyte, wherein at least a portion of the receptor is located on a cell membrane of the living lymphocyte.
31. The composition of claim 30, further comprising a co-receptor on the cell membrane of the living lymphocyte, wherein the co-receptor binds to a portion of the polypeptide molecule.
32. The composition of claim 31, wherein the living lymphocyte is a T cell and the receptor is a T Cell Receptor (TCR).
33. The composition of claim 32, wherein the co-receptor comprises a CD8 molecule.
34. The composition of claim 32, wherein the co-receptor comprises a CD4 molecule.
35. The composition of claim 31, wherein the living lymphocyte is a B cell and the receptor is a B Cell Receptor (BCR).
36. The composition of claim 31, wherein the living cells comprise macrophages and the receptor comprises a chemokine receptor.
37. The composition of claim 31, wherein living cells comprise dendritic cells and the receptor comprises a Pattern Recognition Receptor (PRR).
38. The composition of any one of the preceding claims, wherein the antigenic peptide ranges from 8 to 11 amino acid residues in length.
39. The composition of any one of claims 1 to 37, wherein the antigenic peptide ranges from 15 to 24 residues in length.
40. The composition of any one of the preceding claims, wherein the antigenic peptide comprises a UV moiety.
41. A reaction mixture for generating a probe complex for use in a biological kinetic assay, the mixture comprising:
the composition according to claim 40; and
A target antigen peptide.
42. The reaction mixture of claim 41, wherein said target antigenic peptide is present at a molar excess concentration compared to said antigenic peptide bound to said antigen binding region of said polypeptide molecule.
43. The reaction mixture of any one of claims 41-42, wherein the concentration of the target antigenic peptide is 25-fold greater than the concentration of the antigenic peptide.
44. The reaction mixture of any one of claims 41-43, wherein the reaction mixture comprises 25mM TRIS.
45. The reaction mixture of any one of claims 41-44, wherein the pH of the reaction mixture is 8.0.
46. The reaction mixture of any one of claims 41-45, wherein the reaction mixture comprises 150mM NaCl.
47. The reaction mixture of any one of claims 41-46, wherein the reaction mixture comprises 4mM EDTA.
48. The reaction mixture of any one of claims 41-47, wherein the reaction mixture comprises 5% ethylene glycol.
49. A method of forming a monomeric probe complex, the method comprising:
Contacting a polypeptide molecule comprising an antigen binding region with a first antigenic peptide to generate an antigen presenting complex;
contacting the antigen presenting complex with a plurality of fluorophore molecules to generate a fluorophore-labeled antigen presenting complex;
determining the amount of said fluorophore molecules covalently bound to said fluorophore-labeled antigen presenting complexes; and
Exchanging the first antigenic peptide with a second antigenic peptide to generate the monomeric probe complex.
50. The method of claim 49, wherein exchanging the first antigenic peptide with the second antigenic peptide comprises cleaving the first antigenic peptide to generate a cleaved first antigenic peptide, wherein the cleaved first antigenic peptide has a lower binding affinity for the antigen binding region than the first antigenic peptide.
51. The method of claim 50, wherein cleaving the first antigenic peptide comprises applying UV radiation.
52. The method of claim 50, wherein the second antigenic peptide has a higher affinity for the antigen binding region than the cleaved first antigenic peptide.
53. The method of claim 51, wherein the UV radiation comprises a wavelength of 365 nm.
54. The method of any one of claims 49 to 53, wherein the step of contacting the antigen presenting complex with a plurality of fluorophore molecules to generate fluorophore-labeled antigen presenting complexes comprises covalently linking one or more solvent-exposed surface lysine residues of the polypeptide molecules to one or more of the fluorophore molecules.
55. The method of any one of claims 49 to 54, further comprising separating one or more unconjugated fluorophores from the labeled monomeric probe complex.
56. The method of claim 55, further comprising determining the amount of a plurality of labeled monomeric probe complexes.
57. The method of claim 56, further comprising determining an average number of fluorophores conjugated to each of a plurality of the labeled monomeric probe complexes.
58. The method of claim 57, wherein determining an average number of fluorophores conjugated to each of the plurality of labeled monomeric probe complexes comprises using a plurality of relative abundance values, wherein each relative abundance value corresponds to a different number of conjugated fluorophores.
59. The method of claim 58, wherein each of the plurality of relative abundance values is determined using mass spectrometry.
60. A method for collecting association rate data for assessing living cell activation, the method comprising:
Contacting a plurality of living cells with a plurality of the compositions of any one of claims 1-29 at a concentration, wherein each of the plurality of living cells comprises a plurality of receptor molecules on a cell membrane;
binding the receptor molecules to the composition over a time interval to form a plurality of receptor-probe complexes, wherein each receptor-probe complex comprises a composition that binds to a receptor;
Collecting at least two samples of the plurality of living cells at different points in time within the time interval;
Contacting the living cells in each of the at least two samples with an immobilization agent to preserve the receptor-probe complex and prevent further binding between the receptor molecule and the composition;
Determining the amount of receptor-probe complexes on the cell membrane of each cell; and
Analyzing the amount of receptor-probe complexes on the cell membrane of each cell in each sample to collect the association rate data.
61. A method for collecting dissociation rate data for assessing living cell activation, the method comprising:
Contacting a plurality of living cells with a plurality of the compositions of any one of claims 1-29 at a concentration, wherein each of the plurality of living cells comprises a plurality of receptor molecules on a cell membrane;
binding the receptor molecules to the composition to form a plurality of receptor-probe complexes until equilibrium is reached, wherein each receptor-probe complex comprises a composition that binds to a receptor;
dissociating a portion of the receptor-probe complex over a time interval by reducing the concentration of the composition;
Collecting at least two samples of the plurality of living cells at different points in time within the time interval;
Contacting the living cells in each of the at least two samples with an immobilization agent to preserve the receptor-probe complex and prevent further binding between the receptor molecule and the composition;
Determining the amount of receptor-probe complexes on the cell membrane of each cell; and
Analyzing the amount of receptor-probe complexes on the cell membrane of each cell in each sample to collect the association rate data.
62. The method of any one of claims 60 to 61, wherein the living cells comprise T cells.
63. The method of any one of claims 60 to 61, wherein the living cells comprise B cells.
64. The method of any one of claims 60 to 61, wherein the living cells comprise macrophages.
65. The method of any one of claims 60 to 61, wherein the living cells comprise dendritic cells.
66. The method of any one of claims 60 to 65, wherein the signal strength of the composition is measured using an analytical device.
67. The method of claim 66, wherein the analytical device comprises a flow cytometer.
68. The method of claim 66, wherein the analytical device comprises a fluorometer.
69. The method of any one of claims 60 to 68, wherein the fixative comprises paraformaldehyde.
70. The method of any one of claims 60 to 69, further comprising preventing receptor internalization by lowering the temperature of the receptor-probe complex.
71. The method of claim 70, wherein the temperature is reduced to 4 ℃.
72. The method of any one of claims 60-71, further comprising isolating one or more unbound compositions from the plurality of living cells.
73. The method of any one of claims 60 to 72, wherein each of the receptor-probe complexes comprises a CD8 molecule.
74. The method of any one of claims 60 to 72, wherein each of the receptor-probe complexes comprises a CD4 molecule.
75. The method of any one of claims 60 to 74, further comprising permeabilizing a cell membrane of each cell.
76. The method of claim 75, further comprising applying a detection reagent for detecting the phosphorylation level of the intracellular domain of each of the living cells.
77. The method of claim 76, wherein the intracellular domain comprises a zeta domain.
78. The method of claim 77, wherein said detection reagent comprises an antibody.
79. A system for measuring binding kinetics for assessing living cell activation, the system comprising:
An assay device comprising an assay chamber, wherein the assay chamber comprises a composition according to any one of claims 1 to 40.
80. A system for measuring binding kinetics for assessing living cell activation, the system comprising:
an analysis device comprising an analysis chamber, wherein the analysis chamber comprises a reaction mixture according to any one of claims 41 to 48.
81. The system of any one of claims 79 to 80, wherein the analysis device comprises:
A light source for interrogating the analysis chamber; and
A detector for detecting the signal.
82. The system of claim 81, further comprising a computer system comprising a non-transitory computer-readable storage medium, wherein the non-transitory computer-readable storage medium comprises instructions for analyzing the signal.
83. The system of claim 82, wherein analyzing the signal comprises normalizing the signal with respect to a previously determined calibration value.
84. The system of any one of claims 79 to 83, wherein the analysis chamber comprises a flow cell.
85. The system of any one of claims 80-84, wherein the analysis device comprises a flow cytometer.
86. The system of any one of claims 80-84, wherein the analysis device comprises a fluorometer.
87. The system of any one of claims 80-84, wherein the analysis device comprises a microscope.
88. The system of any one of claims 80 to 84, wherein the analysis device comprises a mass spectrometer.
89. A method for collecting biophysical parameter data for assessing a T Cell Receptor (TCR) association rate constant with a peptide-Major Histocompatibility Complex (MHC), the method comprising:
generating a set of monomeric probes, wherein each monomeric probe comprises a detection molecule and an MHC comprising a peptide;
Associating TCR molecules with the monomeric probes in a one-to-one correspondence to form TCR-monomeric probe complexes over a period of time;
Sampling two or more subsets of TCR-monomer probe complexes over the time interval, wherein each subset is acquired at a different point in time;
preventing the formation of new TCR-monomer probe complexes within each subgroup at their corresponding time points; and
The signal intensity from the detection molecules in each subgroup is measured using an analytical device.
90. The method of claim 89, wherein the TCR molecule is expressed on a T cell.
91. The method of any one of claims 89-90, wherein the detection molecule comprises a fluorescent molecule.
92. The method of any one of claims 89-91, wherein the detection molecule and MHC are coupled by a linker.
93. The method of claim 92, wherein the linker comprises a biotinylated structure.
94. The method of claim 92, wherein the linker comprises PEG.
95. The method of any one of claims 89-94, wherein the analysis device comprises a flow cytometer.
96. The method of any one of claims 89 to 95, wherein the preventing step comprises using a fixing buffer.
97. The method of any one of claims 89-96, further comprising reducing temperature after the preventing step.
98. The method of claim 97, wherein the temperature is 4 degrees celsius.
99. The method of any one of claims 89-98, further comprising isolating unbound monomeric probes from the TCR molecules.
100. The method of any one of claims 89 to 99, wherein the time interval begins before the equilibrium state of the TCR-monomer probe complex.
101. The method of any one of claims 89 to 100, wherein the monomeric probe further comprises a CD8 complex.
102. A method for collecting biophysical parameter data for assessing a T Cell Receptor (TCR) dissociation rate constant with a peptide-major histocompatibility complex (pMHC), the method comprising:
generating a set of monomeric probes, wherein each monomeric probe comprises a detection molecule and an MHC comprising a peptide;
associating TCR molecules with the monomeric probes in a one-to-one correspondence to form TCR-monomeric probe complexes;
dissociating the TCR-monomeric probe complex into monomeric probes and TCRs over a time interval;
Sampling two or more subsets of TCR-monomer probe complexes over the time interval, wherein each subset is acquired at a different point in time;
preventing dissociation of additional TCR-monomer probe complexes within each subgroup at their corresponding time points; and
The signal intensity from the detection molecules in each subgroup is measured using a high throughput analysis device.
103. The method of claim 102, wherein the TCR molecule is expressed on a T cell.
104. The method of any one of claims 102-103, wherein the detection molecule comprises a fluorescent molecule.
105. The method of any one of claims 102 to 104, wherein the detection molecule and MHC are coupled by a linker.
106. The method of claim 105, wherein the linker comprises a biotinylated structure.
107. The method of claim 105, wherein the linker comprises PEG.
108. The method of any one of claims 102-107, wherein the analysis device comprises a flow cytometer.
109. The method of any one of claims 102 to 108, wherein the preventing step comprises using a fixing buffer.
110. The method of any one of claims 102-109, further comprising reducing temperature after the preventing step.
111. The method of claim 110, wherein the temperature is 4 degrees celsius.
112. The method of any one of claims 102-111, further comprising isolating unbound monomeric probes from the TCR molecules.
113. The method of any one of claims 102-112, wherein the time interval begins at an equilibrium state of a TCR-monomer probe complex.
114. The method of any one of claims 102-113, wherein the dissociating step uses a buffer to dilute a solution comprising the TCR-monomer probe complex.
115. The method of any one of claims 102-114, wherein the monomeric probe further comprises a CD8 complex.
Applications Claiming Priority (2)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US63/287,012 | 2021-12-07 | ||
| US63/397,325 | 2022-08-11 |
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| Publication Number | Publication Date |
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| CN118355277A true CN118355277A (en) | 2024-07-16 |
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