Patent Application
20230349919
This application includes a Sequence Listing filed electronically as an XML file named 381203732SEQ, created on Mar. 10, 2023, with a size of 824 kilobytes. The Sequence Listing is incorporated herein by reference.
The present disclosure is directed, in part, to antibody capture complexes and methods of mapping antigen specificity to antibody-secreting cells.
B cells express the B cell receptor (BCR) on their surface, thereby allowing the determination of an antigen-specific B cell repertoire profiling. While multiple platforms are available for antibody discovery from B cells expressing cell-surface BCR, the antibodies isolated vary from low to high affinity. Following activation by cognate antigen, B cells undergo fine-tuning of their BCRs and may ultimately differentiate into antibody-secreting cells (ASCs). Antibody secreting cells are a specialized cell type that represents the end-stage of the B-cell differentiation program and comprise plasmablasts, short-lived plasma cells, and long-lived plasma cells (or, more commonly, simply “plasma cells” (PCs); Tellier and Nutt, Eur. J. Immunol., 2019, 49, 30-37). These ASCs can produce high-affinity antibodies with therapeutic or prophylactic potential. However, ASCs can also be the source of antibody-mediated pathologies.
While antigen-specific antibodies from B cells expressing BCRs on their cell surface can be readily cloned and sequenced following flow cytometric isolation, PCs, which are ASCs that do not express cell-surface BCRs, cannot currently be easily profiled in a high-throughput way. And while PCs may be the source of very high-affinity antibody, the specificity of any given secreted antibody cannot rapidly be determined. Because there are limitations as to the application of current platforms to PCs, there is a long-felt but unsolved need to efficiently pair a given antibody with the BCR− PC that secreted it as well as to efficiently determine the antigen specificity of that antibody.
The present disclosure provides an antibody capture complex comprising a first component of a binding pair linked to an antibody-capture molecule; wherein the first component of the binding pair is capable of binding a second component of the binding pair; wherein the antibody-capture molecule is capable of binding to a target antibody, wherein the target antibody is secreted by an antibody secreting cell. In some embodiments, when the second component of the binding pair is biotin and the first component of the binding pair is streptavidin, the antibody-capture molecule does not bind to a kappa light chain of the target antibody.
The present disclosure also provides methods of capturing a target antibody secreted by an antibody secreting cell, the methods comprising: contacting a population of antibody secreting cells with a second component of a binding pair to allow the second component of the binding pair to bind to the cell surface of the population of antibody secreting cells, wherein the population of antibody secreting cells comprises the antibody secreting cell that secretes the target antibody; contacting the population of antibody secreting cells with an antibody capture complex, wherein the antibody capture complex comprises a first component of the binding pair linked to an antibody-capture molecule, whereby the first component of the binding pair binds to the second component of the binding pair on the cell surface of the antibody secreting cells, and whereby the antibody-capture molecule captures the target antibody secreted by the antibody secreting cell; and contacting the population of antibody secreting cells with an antigen, whereby the target antibody secreted by the antibody secreting cell and captured by the antibody capture complex binds the antigen.
The present disclosure also provides methods of capturing a target antibody secreted by an antibody secreting cell, the methods comprising: contacting a population of antibody secreting cells with an antibody capture complex, wherein the population of antibody secreting cells comprises the antibody secreting cell that secretes the target antibody, wherein the antibody capture complex comprises a first component of a binding pair linked to an antibody-capture molecule, whereby the first component of the binding pair binds to a second component of the binding pair on the cell surface of the population of antibody secreting cells, and whereby the antibody-capture molecule captures the target antibody secreted by the antibody secreting cell; and contacting the population of antibody secreting cells with an antigen, whereby the target antibody secreted by the antibody secreting cell and captured by the antibody capture complex binds the antigen.
The present disclosure also provides methods of capturing an IgE antibody secreted by an antibody secreting cell, wherein the IgE antibody is directed to an allergen, the methods comprising: contacting a population of antibody secreting cells with NHS-biotin to allow biotin to bind to the cell surface, wherein the population of antibody secreting cells comprises the antibody secreting cell that secretes the IgE antibody; contacting the population of antibody secreting cells with an antibody capture complex, wherein the antibody capture complex comprises streptavidin linked to an ectodomain of a high affinity IgE receptor (FcεRIa), whereby the antibody-capture molecule binds to the IgE antibody secreted by the antibody secreting cell; and contacting the population of antibody secreting cells with an antigen, wherein the antigen is an antigenic portion or a mixture of a plurality of antigenic portions of the allergen, whereby the IgE antibody captured by the antibody capture complex binds to the antigen.
In some embodiments of the methods disclosed herein, the methods further comprise, after contacting the population of antibody secreting cells with an antigen, sorting the antibody secreting cells to collect a pool of antibody secreting cells, wherein the antibody secreting cells in the pool each secrete an antibody that is captured by the antibody capture molecule and is bound by the antigen, wherein the collected pool of antibody secreting cells comprises the antibody secreting cell that secretes the target antibody. In some embodiments of the methods disclosed herein, the methods further comprise separating the collected pool of antibody secreting cells into single cells and isolating the antibody secreting cell that secretes the target antibody. In some embodiments, antibody-encoding nucleic acids are isolated from the antibody secreting cell that secretes the target antibody.
In some embodiments of the methods disclosed herein, the step of contacting the population of antibody secreting cells with an antigen comprises: (a) contacting the population of antibody secreting cells with a first labeled form of the antigen to allow the antigen to bind to antibodies captured at the cell surface of the population of antibody secreting cells including the target antibody captured on the cell surface of the antibody secreting cell, wherein the antigen of the first labeled form is conjugated to a first detectable label; (b) washing the population of antibody secreting cells to remove unbound antigen; (c) contacting the population of antibody secreting cells with (i) an unlabeled form of the antigen, (ii) a second labeled form of the antigen, or (iii) the unlabeled form of the antigen and the second labeled form of the antigen; (d) washing the population of antibody secreting cells to remove unbound antigen, and (e) collecting a pool of antibody secreting cells remaining bound to the first labeled form of the antigen, wherein the collected pool of antibody secreting cells comprises the antibody secreting cell that secretes the target antibody, and wherein the target antibody secreted by the antibody secreting cell and captured by the antibody capture complex remains bound to the first labeled form of the antigen.
In some embodiments of the methods disclosed herein, after collecting a pool of antibody secreting cells remaining bound to the first labeled form of the antigen, the methods further comprise separating the collected pool of antibody secreting cells into single cells and isolating the antibody secreting cell that secretes the target antibody. In some embodiments, antibody-encoding nucleic acids are isolated from the antibody secreting cell that secretes the target antibody.
The present disclosure also provides methods of identifying a region of a gene encoding an antigen-binding fragment of a target antibody wherein the target antibody is secreted by a cell comprising a modified cell surface, and wherein the target antibody is subsequently captured on the modified cell surface, the methods comprising: a) providing an antibody secreting cell comprising a modified cell surface, wherein the antibody secreting cell secretes a target antibody, wherein the target antibody is subsequently captured on the modified cell surface, wherein the target antibody captured on the modified cell surface is bound to an antigen, wherein the antigen is linked to a barcode nucleic acid molecule, and wherein the antibody secreting cell further comprises a nucleic acid molecule comprising the region of the gene encoding the antigen-binding fragment of the target antibody captured on the modified cell surface; b) hybridizing a portion of the barcode nucleic acid molecule to a portion of a first nucleic acid molecule attached to a solid surface; c) hybridizing a portion of the nucleic acid molecule comprising the region of the gene encoding the antigen-binding fragment of the target antibody captured on the modified cell surface to a portion of a second nucleic acid molecule attached to the solid surface; d) preparing a first library of amplicons of gene expression in the antibody secreting cell, a second library of amplicons of variable regions, diversity regions, and joining regions (VDJ) in the antibody secreting cell, and a third library of amplicons of antigen barcode nucleic acid molecules; e) sequencing each of the three libraries of amplicons; and f) identifying the region of the gene encoding the antigen-binding fragment of the target antibody captured on the modified cell surface.
The present disclosure also provides methods of identifying a region of a gene encoding an antigen-binding fragment of a target antibody, wherein the target antibody is secreted by an antibody secreting cell, the methods comprising: a) contacting a population of antibody secreting cells with a second component of a binding pair to allow the second component of the binding pair to bind to the cell surface, wherein the population of antibody secreting cells comprises the antibody secreting cell that secretes the target antibody; b) contacting the population of antibody secreting cells with an antibody capture complex, wherein the antibody capture complex comprises a first component of the binding pair linked to an antibody-capture molecule, whereby the first component of the binding pair binds to the second component of the binding pair on the cell surface of the population of antibody secreting cells, and whereby the antibody-capture molecule captures the target antibody secreted by the antibody secreting cell; c) contacting the population of antibody secreting cells with a secondary anti-Ig antibody, whereby the target antibody secreted by the antibody secreting cell and captured by the antibody capture complex binds the secondary anti-Ig antibody; d) contacting the population of antibody secreting cells with an antigen comprising a barcode nucleic acid molecule, whereby the target antibody secreted by the antibody secreting cell and captured by the antibody capture complex binds the antigen; e) collecting a pool of antibody secreting cells, wherein each cell in the pool secretes an antibody that is captured by the antibody capture complex, bound by the secondary anti-Ig antibody and by the antigen comprising the barcode nucleic acid molecule, and wherein the pool of antibody secreting cells comprises the antibody secreting cell that secretes the target antibody; f) separating the pool of antibody secreting cells into single antibody secreting cells, and for each single antibody secreting cell: 1) hybridizing a portion of the barcode nucleic acid molecule to a portion of a first nucleic acid molecule attached to a solid surface, wherein the solid surface and the first nucleic acid molecule attached thereto are unique to each single antibody secreting cell; 2) hybridizing a portion of the nucleic acid molecule comprising the region of the gene encoding the antigen-binding fragment of the target antibody to a portion of a second nucleic acid molecule attached to the solid surface; 3) preparing a first library of amplicons of gene expression, a second library of amplicons of variable regions, diversity regions, and joining regions (VDJ), and a third library of amplicons of antigen barcode nucleic acid molecules; and 4) sequencing each of the three libraries of amplicons; and g) identifying the region of the gene encoding the antigen-binding fragment of the target antibody.
The present disclosure also provides methods of identifying a region of a gene encoding an antigen-binding fragment of a target antibody, wherein the target antibody is secreted by an antibody secreting cell, the methods comprising: a) contacting a population of antibody secreting cells with an antibody capture complex, wherein the population of antibody secreting cells comprises the antibody secreting cell that secretes the target antibody, wherein the antibody capture complex comprises a first component of a binding pair linked to an antibody-capture molecule, whereby the first component of the binding pair binds to a second component of the binding pair on the cell surface of the population of antibody secreting cells, and whereby the antibody-capture molecule captures the target antibody secreted by the antibody secreting cell; b) contacting the population of antibody secreting cells with a secondary anti-Ig antibody, whereby the target antibody secreted by the antibody secreting cell and captured by the antibody capture complex binds the secondary anti-Ig antibody; c) contacting the population of antibody secreting cells with an antigen comprising a barcode nucleic acid molecule, whereby the target antibody secreted by the antibody secreting cell and captured by the antibody capture complex binds the antigen; d) collecting a pool of antibody secreting cells, wherein each cell in the pool secretes an antibody that is captured by the antibody capture complex, bound by the secondary anti-Ig antibody and by the antigen comprising the barcode nucleic acid molecule, and wherein the pool of antibody secreting cells comprises the antibody secreting cell that secretes the target antibody; e) separating the pool of antibody secreting cells into single antibody secreting cells, and for each single antibody secreting cell: 1) hybridizing a portion of the barcode nucleic acid molecule to a portion of a first nucleic acid molecule attached to a solid surface, wherein the solid surface and the first nucleic acid molecule attached thereto are unique to each single antibody secreting cell; 2) hybridizing a portion of the nucleic acid molecule encoding the region of the gene encoding the antigen-binding fragment of the target antibody to a portion of a second nucleic acid molecule attached to the solid surface; 3) preparing a first library of amplicons of gene expression, a second library of amplicons of variable regions, diversity regions, and joining regions (VDJ), and a third library of amplicons of antigen barcode nucleic acid molecules; and 4) sequencing each of the three libraries of amplicons; and f) identifying the region of the gene encoding the antigen-binding fragment of the target antibody.
The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.
The terminology used herein is for the purpose of describing particular embodiments only and is not intended to be limiting.
Various terms relating to aspects of the present disclosure are used throughout the specification and claims. Such terms are to be given their ordinary meaning in the art, unless otherwise indicated. Other specifically defined terms are to be construed in a manner consistent with the definitions provided herein.
Unless otherwise expressly stated, it is not intended that any method or aspect set forth herein be construed as requiring that its steps be performed in a specific order. Accordingly, where a method claim does not specifically state in the claims or descriptions that the steps are to be limited to a specific order, it is not intended that an order be inferred, in any respect. This holds for any possible non-expressed basis for interpretation, including matters of logic with respect to arrangement of steps or operational flow, plain meaning derived from grammatical organization or punctuation, or the number or type of aspects described in the specification.
As used herein, the singular forms “a,” “an” and “the” include plural referents unless the context clearly dictates otherwise.
As used herein, the term “about” means that the recited numerical value is approximate and small variations would not significantly affect the practice of the disclosed embodiments. Where a numerical value is used, unless indicated otherwise by the context, the term “about” means the numerical value can vary by ±10% and remain within the scope of the disclosed embodiments.
As used herein, the term “comprising” may be replaced with “consisting” or “consisting essentially of” in particular embodiments as desired.
As used herein, the terms “nucleic acid”, “nucleic acid molecule”, “nucleic acid sequence”, “polynucleotide”, or “oligonucleotide” can comprise a polymeric form of nucleotides of any length, can comprise DNA and/or RNA, and can be single-stranded, double-stranded, or multiple stranded. One strand of a nucleic acid also refers to its complement.
As used herein, the term “antibody” can comprise an intact immunoglobulin molecule, a fragmented immunoglobulin molecule comprising an antigen-binding fragment, an antigen-binding fragment without any other fragment of an immunoglobulin molecule.
The present disclosure provides antibody capture complexes comprising a first component of a binding pair linked to an antibody-capture molecule; wherein the first component of the binding pair is capable of binding a second component of the binding pair; wherein the antibody-capture molecule is capable of binding to a target antibody, wherein the target antibody is secreted by an antibody secreting cell. In some embodiments, when the second component of the binding pair is biotin and the first component of the binding pair is streptavidin, the antibody-capture molecule does not bind to a kappa light chain of the target antibody.
In some embodiments, a first component of a binding pair comprises a first reagent and a second component comprises a second reagent, wherein the first reagent and the second reagent form a bond.
In some embodiments, the first component of the binding pair comprises avidin, streptavidin, or anti-biotin, and the second component of the binding pair comprises biotin. In some embodiments, the first component of the binding pair comprises biotin and the second component of the binding pair comprises avidin and/or streptavidin. In some embodiments, the first component of the binding pair comprises biotin and the second component of the binding pair comprises anti-biotin. In some embodiments, the first component of the binding pair comprises one of jun and fos and the second component of the binding pair comprises the other of jun and fos. In some embodiments, the first component of the binding pair comprises one of mad and max and the second component of the binding pair comprises the other of mad and max. In some embodiments, the first component of the binding pair comprises one of myc and max and the second component of the binding pair comprises the other of myc and max. In some embodiments, the first component of the binding pair comprises one of an azide and an alkyne and the second component of the binding pair comprises the other of an azide and an alkyne. In some embodiments, the first component of the binding pair comprises one of an azide and a phosphine and the second component of the binding pair comprises the other of an azide and a phosphine.
In some embodiments, the second component of the binding pair comprises a surface marker of the antibody secreting cell and the first component of the binding pair comprises an antibody that binds to the surface marker. In some embodiments, the cell surface marker comprises CD27, CD38, CD45, CD138, CD98, CD78, CD319, CXCR4, BCMA, GPRC5D, FCRL5, CD19, Ly6D, CD52, or transmembrane activator calcium modulator and cyclophilin ligand interactor (TACI). In some embodiments, the cell surface marker comprises CD27. In some embodiments, the cell surface marker comprises CD38. In some embodiments, the cell surface marker comprises CD45. In some embodiments, the cell surface marker comprises CD138. In some embodiments, the cell surface marker comprises CD98. In some embodiments, the cell surface marker comprises CD78. In some embodiments, the cell surface marker comprises CD319. In some embodiments, the cell surface marker comprises CXCR4. In some embodiments, the cell surface marker comprises BCMA. In some embodiments, the cell surface marker comprises GPRC5D. In some embodiments, the cell surface marker comprises FCRL5. In some embodiments, the cell surface marker comprises CD19. In some embodiments, the cell surface marker comprises Ly6D. In some embodiments, the cell surface marker comprises CD52. In some embodiments, the cell surface marker comprises TACI.
In some embodiments, the second component of the binding pair comprises an interleukin-6 receptor (IL-6R), and the first component of the binding pair comprises an anti-IL-6R antibody, interleukin-6 (IL-6), and/or a fragment of IL-6 capable of binding to IL-6R. In some embodiments, the second component of the binding pair comprises CD27, and the first component of the binding pair comprises an anti-CD27 antibody, CD70, and/or a fragment of CD70 capable of binding to CD27.
In some embodiments, the second component of the binding pair comprises fluorescein isothiocyanate (FITC) and the first component of the binding pair comprises an anti-FITC antibody. In some embodiments, the second component of the binding pair comprises fluorescein and the first component of the binding pair comprises an anti-fluorescein antibody. In some embodiments, the second component of the binding pair comprises phycoerythrin (PE), and the first component of the binding pair comprises an anti-PE antibody. In some embodiments, the second component of the binding pair comprises APC, and the first component of the binding pair comprises an anti-APC antibody. In some embodiments, the second component of the binding pair comprises BV421, and the first component of the binding pair comprises an anti-BV421 antibody. In some embodiments, the second component of the binding pair comprises BV510, and the first component of the binding pair comprises an anti-BV510 antibody. In some embodiments, the second component of the binding pair comprises BV605, and the first component of the binding pair comprises an anti-BV605 antibody. In some embodiments, the second component of the binding pair comprises BV650, and the first component of the binding pair comprises an anti-BV650 antibody. In some embodiments, the second component of the binding pair comprises BV711, and the first component of the binding pair comprises an anti-BV711 antibody. In some embodiments, the second component of the binding pair comprises BV786, and the first component of the binding pair comprises an anti-BV786 antibody.
In some embodiments, the antibody-capture molecule comprises a capture antibody.
In some embodiments, the capture antibody comprises an anti-Fc antibody. In some embodiments, the capture antibody comprises an anti-Fcγ antibody, an anti-Fcα antibody, or an anti-Fcε antibody. In some embodiments, the capture antibody comprises an anti-Fcγ antibody. In some embodiments, the capture antibody comprises an anti-Fcα antibody. In some embodiments, the capture antibody comprises an anti-Fcε antibody. In some embodiments, the anti-Fcγ antibody comprises an anti-FcγRI antibody, an anti-FcγRIIA antibody, an anti-FcγRIIB antibody, an anti-FcγRIIB1 antibody, an anti-FcγRIIB2 antibody, an anti-FcγRIIIA antibody, and/or an anti-FcγRIIIB antibody. In some embodiments, the anti-Fcγ antibody comprises an anti-FcγRI antibody. In some embodiments, the anti-Fcγ antibody comprises an anti-FcγRIIA antibody. In some embodiments, the anti-Fcγ antibody comprises an anti-FcγRIIB antibody. In some embodiments, the anti-Fcγ antibody comprises an anti-FcγRIIB1 antibody. In some embodiments, the anti-Fcγ antibody comprises an anti-FcγRIIB2 antibody. In some embodiments, the anti-Fcγ antibody comprises an anti-FcγRIIIA antibody. In some embodiments, the anti-Fcγ antibody comprises an anti-FcγRIIIB antibody. In some embodiments, the anti-Fcα antibody comprises an anti-FcαRI antibody. In some embodiments, the anti-Fcε antibody comprises an anti-FcεRI antibody or an anti-FcεRIII antibody. In some embodiments, the anti-Fcε antibody comprises an anti-FcεRI antibody. In some embodiments, the anti-Fcε antibody comprises an anti-FcεRII antibody.
In some embodiments, the capture antibody comprises an anti-light chain kappa antibody and/or an anti-light chain lambda antibody. In some embodiments, the capture antibody comprises an anti-light chain kappa antibody. In some embodiments, the capture antibody comprises an anti-light chain lambda antibody.
In some embodiments, the capture antibody comprises an anti-Ig antibody.
In some embodiments, the capture antibody comprises an anti-IgM antibody.
In some embodiments, the capture antibody comprises an anti-IgG antibody. In some embodiments, the anti-IgG antibody comprises an anti-IgG1 antibody, an anti-IgG2 antibody, an anti-IgG2a antibody, an anti-IgG2b antibody, an anti-IgG3 antibody, and/or an anti-IgG4 antibody. In some embodiments, the anti-IgG antibody comprises an anti-IgG1 antibody. In some embodiments, the anti-IgG antibody comprises an anti-IgG2 antibody. In some embodiments, the anti-IgG antibody comprises an anti-IgG2a antibody. In some embodiments, the anti-IgG antibody comprises an anti-IgG2b antibody. In some embodiments, the anti-IgG antibody comprises an anti-IgG3 antibody. In some embodiments, the anti-IgG antibody comprises an anti-IgG4 antibody.
In some embodiments, the capture antibody comprises an anti-IgA antibody. In some embodiments, the anti-IgA antibody comprises an anti-IgA1 antibody, an anti-IgA2 antibody, an anti-secretory IgA antibody, or a polymeric anti-IgA antibody. In some embodiments, the anti-IgA antibody comprises an anti-IgA1 antibody. In some embodiments, the anti-IgA antibody comprises an anti-IgA2 antibody. In some embodiments, the anti-IgA antibody comprises an anti-secretory IgA antibody. In some embodiments, the anti-IgA antibody comprises a polymeric anti-IgA antibody.
In some embodiments, the capture antibody comprises an anti-IgE antibody.
In some embodiments, the antibody-capture molecule comprises an Fc receptor or an ectodomain of the Fc receptor. In some embodiments, the Fc receptor comprises an Fcγ receptor, an Fcα receptor, and/or an Fcε receptor. In some embodiments, the Fc receptor comprises an Fcγ receptor. In some embodiments, the Fc receptor comprises an Fcα receptor. In some embodiments, the Fc receptor comprises an Fcε receptor. In some embodiments, the Fcγ receptor comprises an FcγRI receptor, an FcγRIIA receptor, an FcγRIIB receptor, an FcγRIIB1 receptor, an FcγRIIB2 receptor, an FcγRIIIA receptor, an FcγRIIIB receptor, and/or an FcRn receptor. In some embodiments, the Fcγ receptor comprises an FcγRI receptor. In some embodiments, the Fcγ receptor comprises an FcγRIIA receptor. In some embodiments, the Fcγ receptor comprises an FcγRIIB receptor. In some embodiments, the Fcγ receptor comprises an FcγRIIB1 receptor. In some embodiments, the Fcγ receptor comprises an FcγRIIB2 receptor. In some embodiments, the Fcγ receptor comprises an FcγRIIIA receptor. In some embodiments, the Fcγ receptor comprises an FcγRIIIB receptor. In some embodiments, the Fcγ receptor comprises an FcRn receptor. In some embodiments, the Fcα receptor comprises an FcαRI receptor and/or an Fcα/μR receptor. In some embodiments, the Fcα receptor comprises an FcαRI receptor. In some embodiments, the Fcα receptor comprises an Fcα/μR receptor. In some embodiments, the Fcε receptor comprises an FcεRI receptor and/or an FcεRII receptor. In some embodiments, the Fcε receptor comprises an FcεRI receptor. In some embodiments, the Fcε receptor comprises an FcεRII receptor. In some embodiments, the Fc receptor comprises a fragment of an Fc receptor capable of binding Fc.
In some embodiments, the antibody-capture molecule comprises protein A, a fragment of protein A capable of binding to a portion of an Fc region, protein G, and/or a fragment of protein G capable of binding to a portion of an Fc region. In some embodiments, the antibody-capture molecule comprises protein A. In some embodiments, the antibody-capture molecule comprises a fragment of protein A capable of binding to a portion of an Fc region. In some embodiments, the antibody-capture molecule comprises protein G. In some embodiments, the antibody-capture molecule comprises a fragment of protein G capable of binding to a portion of an Fc region. In some embodiments, the antibody-capture molecule comprises protein L and/or a fragment of protein L capable of binding to a portion of a light chain. In some embodiments, the antibody-capture molecule comprises protein L. In some embodiments, the antibody-capture molecule comprises a fragment of protein L capable of binding to a portion of a light chain.
In some embodiments, the antibody capture complex comprises avidin or streptavidin linked to an ectodomain of a high affinity IgE receptor (FcεRIa). In some embodiments, the antibody capture complex comprises avidin linked to FcεRIa. In some embodiments, the antibody capture complex comprises streptavidin linked to FcεRIa.
In some embodiments, the target antibody comprises an IgM antibody.
In some embodiments, the target antibody comprises an IgG antibody. In some embodiments, the anti-IgG antibody comprises an IgG1 antibody, an IgG2 antibody, an IgG2a antibody, an IgG2b antibody, an IgG3 antibody, and/or an IgG4 antibody. In some embodiments, the anti-IgG antibody comprises an IgG1 antibody. In some embodiments, the anti-IgG antibody comprises an IgG2 antibody. In some embodiments, the anti-IgG antibody comprises an IgG2a antibody. In some embodiments, the anti-IgG antibody comprises an IgG2b antibody. In some embodiments, the anti-IgG antibody comprises an IgG3 antibody. In some embodiments, the anti-IgG antibody comprises an IgG4 antibody.
In some embodiments, the target antibody comprises an IgA antibody. In some embodiments, the IgA antibody comprises an IgA1 antibody, an IgA2 antibody, a secretory IgA antibody, or a polymeric IgA antibody. In some embodiments, the IgA antibody comprises an IgA1 antibody. In some embodiments, the IgA antibody comprises an IgA2 antibody. In some embodiments, the IgA antibody comprises a secretory IgA antibody. In some embodiments, the IgA antibody comprises a polymeric IgA antibody.
In some embodiments, the target antibody comprises an IgE antibody.
In some embodiments, the target of the target antibody, i.e., the antigen to which the target antibody binds, is an allergen. In some embodiments, the allergen comprises a component of an animal product, a drug, a foodstuff, a substance present in a venom, a substance present in saliva of a biting insect, a mold spore, a cosmetic, a metal, latex, a wood, and/or a plant pollen. In some embodiments, the allergen comprises a component of an animal product. In some embodiments, the allergen comprises a drug. In some embodiments, the allergen comprises a foodstuff. In some embodiments, the allergen comprises a substance present in a venom. In some embodiments, the allergen comprises a substance present in saliva of a biting insect. In some embodiments, the allergen comprises a mold spore. In some embodiments, the allergen comprises a cosmetic. In some embodiments, the allergen comprises a metal. In some embodiments, the allergen comprises latex. In some embodiments, the allergen comprises a wood. In some embodiments, the allergen comprises a plant pollen.
In some embodiments, the animal product comprises Bla g, Bla g 1, Bla g 2, Bla g 3, Bla g 3, Bla g 4, Bla g 5, Bla g 6, Bla g 7, Bla g 8, Bla g 9, Bla g 11, Per a, Per a 1, Per a 2, Per a 3, Per a 6, Per a 7, Per a 9, Per a 10, Per a 11, Per a 12, Der p 1, Der p 2, Der f 1, Eur m 1, Pso o 1, Equ c 1, Fel d 1, Fel d 4, Mus m 1, Rat n 1, dust mite tropomyosin, shellfish tropomyosin, and/or cockroach tropornyosin. In some embodiments, the animal product comprises Bla g. In some embodiments, the animal product comprises Bla g 1. In some embodiments, the animal product comprises Bla g 2. In some embodiments, the animal product comprises Bla g 3. In some embodiments, the animal product comprises Bla g 3. In some embodiments, the animal product comprises Bla g 4. In some embodiments, the animal product comprises Bla g 5. In some embodiments, the animal product comprises Bla g 6. In some embodiments, the animal product comprises Bla g 7. In some embodiments, the animal product comprises Bla g 8. In some embodiments, the animal product comprises Bla g 9. In some embodiments, the animal product comprises Bla g 11. In some embodiments, the animal product comprises Per a. In some embodiments, the animal product comprises, Per a 1. In some embodiments, the animal product comprises Per a 2. In some embodiments, the animal product comprises Per a 3. In some embodiments, the animal product comprises Per a 6. In some embodiments, the animal product comprises Per a 7. In some embodiments, the animal product comprises Per a 9. In some embodiments, the animal product comprises Per a 10. In some embodiments, the animal product comprises Per a 11. In some embodiments, the animal product comprises Per a 12. In some embodiments, the animal product comprises Der p 1. In some embodiments, the animal product comprises Der p 2. In some embodiments, the animal product comprises Der f 1. In some embodiments, the animal product comprises Eur m 1. In some embodiments, the animal product comprises Pso o 1. In some embodiments, the animal product comprises Equ c 1. In some embodiments, the animal product comprises Fel d 1. In some embodiments, the animal product comprises Fel d 4. In some embodiments, the animal product comprises Mus m 1. In some embodiments, the animal product comprises Rat n 1. In some embodiments, the animal product comprises dust mite tropomyosin. In some embodiments, the animal product comprises shellfish tropomyosin. In some embodiments, the animal product comprises cockroach tropomyosin.
In some embodiments, the animal product comprises animal fur, animal dander, cockroach calyx, wool, and/or a dust mite secretion. In some embodiments, the animal product comprises animal fur. In some embodiments, the animal product comprises animal dander. In some embodiments, the animal product comprises cockroach calyx. In some embodiments, the animal product comprises wool. In some embodiments, the animal product comprises a dust mite secretion.
In some embodiments, the drug comprises penicillin, a sulfonamide, a salicylate, and/or neomycin. In some embodiments, the drug comprises penicillin. In some embodiments, the drug comprises a sulfonamide. In some embodiments, the drug comprises a salicylate. In some embodiments, the drug comprises neomycin.
In some embodiments, the foodstuff comprises celery, celeriac, corn, maize, egg, fruit, pumpkin, eggplant, legume, milk, seafood, sesame, soy, tree nut, wheat, and/or balsam of Peru. In some embodiments, the foodstuff comprises celery. In some embodiments, the foodstuff comprises celeriac. In some embodiments, the foodstuff comprises corn. In some embodiments, the foodstuff comprises maize. In some embodiments, the foodstuff comprises egg. In some embodiments, the foodstuff comprises fruit. In some embodiments, the foodstuff comprises pumpkin. In some embodiments, the foodstuff comprises eggplant. In some embodiments, the foodstuff comprises legume. In some embodiments, the foodstuff comprises milk. In some embodiments, the foodstuff comprises seafood. In some embodiments, the foodstuff comprises sesame. In some embodiments, the foodstuff comprises soy. In some embodiments, the foodstuff comprises tree nut. In some embodiments, the foodstuff comprises wheat. In some embodiments, the foodstuff comprises balsam of Peru. In some embodiments, the legume comprises a bean, a pea, a peanut, or a soybean. In some embodiments, the legume comprises a bean. In some embodiments, the legume comprises a pea. In some embodiments, the legume comprises a peanut. In some embodiments, the legume comprises a soybean. In some embodiments, the tree nut comprises a pecan and/or an almond. In some embodiments, the tree nut comprises a pecan. In some embodiments, the tree nut comprises an almond.
In some embodiments, the substance present in a venom comprises a substance present in bee sting venom and/or a substance present in wasp sting venom. In some embodiments, the substance present in a venom comprises a substance present in bee sting venom. In some embodiments, the substance present in a venom comprises a substance present in wasp sting venom.
In some embodiments, the biting insect is a mosquito or tick. In some embodiments, the biting insect is a mosquito. In some embodiments, the biting insect is a tick. In some embodiments, the allergen in the biting insect is present in the saliva. In some embodiments, the allergen comprises an oligosaccharide. In some embodiments, the allergen comprises galactose-alpha-1,3-galactose or galactose-alpha-1,3-galactose-beta-1,4-N-acetyl glucosamine.
In some embodiments, the cosmetic comprises a fragrance and/or quaternium-15. In some embodiments, the cosmetic comprises a fragrance. In some embodiments, the cosmetic comprises quaternium-15.
In some embodiments, the metal comprises nickel and/or chromium. In some embodiments, the metal comprises nickel. In some embodiments, the metal comprises chromium.
In some embodiments, the plant pollen comprises a grass pollen, a weed pollen, and/or a tree pollen. In some embodiments, the plant pollen comprises a grass pollen. In some embodiments, the plant pollen comprises a weed pollen. In some embodiments, the plant pollen comprises a tree pollen. In some embodiments, the grass pollen comprises ryegrass pollen and/or timothy-grass pollen. In some embodiments, the grass pollen comprises ryegrass pollen. In some embodiments, the grass pollen comprises timothy-grass pollen. In some embodiments, the weed pollen comprises ragweed pollen, plantago pollen, nettle pollen, pollen of the species Artemisia vulgaris, pollen of the species Chenopodium album, or sorrel pollen. In some embodiments, the weed pollen comprises ragweed pollen. In some embodiments, the weed pollen comprises plantago pollen. In some embodiments, the weed pollen comprises nettle pollen. In some embodiments, the weed pollen comprises pollen of the species Artemisia vulgaris. In some embodiments, the weed pollen comprises pollen of the species Chenopodium album. In some embodiments, the weed pollen comprises sorrel pollen. In some embodiments, the tree pollen comprises birch pollen, alder pollen, hazel pollen, hornbeam pollen, pollen of the genus Aesculus, willow pollen, poplar pollen, pollen of the genus Platanus, pollen of the genus Tilia, pollen of the species Olea, pollen of Ashe juniper, or pollen of the species Alstonia scholaris. In some embodiments, the tree pollen comprises birch pollen. In some embodiments, the tree pollen comprises alder pollen. In some embodiments, the tree pollen comprises hazel pollen. In some embodiments, the tree pollen comprises hornbeam pollen. In some embodiments, the tree pollen comprises pollen of the genus Aesculus. In some embodiments, the tree pollen comprises willow pollen. In some embodiments, the tree pollen comprises poplar pollen. In some embodiments, the tree pollen comprises pollen of the genus Platanus. In some embodiments, the tree pollen comprises pollen of the genus Tilia. In some embodiments, the tree pollen comprises pollen of the species Olea. In some embodiments, the tree pollen comprises pollen of Ashe juniper. In some embodiments, the tree pollen comprises pollen of the species Alstonia scholaris. In some embodiments, the plant pollen comprises olive tree pollen. In some embodiments, the allergen comprises Ole e 1.
In some embodiments, the allergen comprises is one from an oak tree (Quercus albus), Japanese cedar tree (Cryptomeria japonica), or from an Elm tree or Hickory tree.
In some embodiments, the allergen comprises a dog allergen, such as Can f proteins. In some embodiments, the allergen comprises a cow's milk allergen or a beef protein, such as Bos d 2-13. In some embodiments, the allergen comprises a chicken allergen (e.g., Gal d proteins), pig allergens (i.e., Sus s proteins), or a serum albumin. In some embodiments, the allergen comprises a fish allergen (e.g., Gad c/Gad m/Pan h/Sals s proteins) In some embodiments, the allergen comprises a parvalbumin.
In any of the embodiments described herein, the allergen can be replaced with a non-allergen compound such as, for example, a foreign antigen. In some embodiments, the foreign antigen comprises a spike protein of a coronavirus. In some embodiments, the foreign antigen comprises a mutated peptide from a host. In some embodiments, the foreign antigen comprises a protein from another species. In some embodiments, the foreign antigen comprises a compound from an infectious disease, such as SARS-CoV-2 or influenza virus.
In some embodiments, the antibody secreting cell is a plasma cell. In some embodiments, the antibody secreting cell is a plasmablast. In some embodiments, the plasma cell is a short-lived plasma cell. In some embodiments, the plasma cell is a long-lived plasma cell.
The present disclosure also provides methods of capturing a target antibody secreted by an antibody secreting cell, the method comprising: contacting a population of antibody secreting cells with a second component of a binding pair to allow the second component of the binding pair to bind to the cell surface, wherein the population of antibody secreting cells comprises the antibody secreting cell that secretes the target antibody; contacting the population of antibody secreting cells with an antibody capture complex, wherein the antibody capture complex comprises a first component of the binding pair linked to an antibody-capture molecule, whereby the first component of the binding pair binds to the second component of the binding pair on the cell surface of the antibody secreting cells, and whereby the antibody-capture molecule captures the target antibody secreted by the antibody secreting cell; and contacting the population of antibody secreting cells with an antigen to allow the target antibody secreted by the antibody secreting cell and captured by the antibody capture complex to bind the antigen. In some embodiments, the method further comprises, after contacting the population of antibody secreting cells with an antibody capture complex, contacting the population of antibody secreting cells with a secondary anti-Ig antibody. The step of contacting with a secondary anti-Ig antibody can be performed before, with, or after the step of contacting the population of antibody secreting cells with an antigen.
The present disclosure also provides methods of capturing a target antibody secreted by an antibody secreting cell, the method comprising: contacting a population of antibody secreting cells with an antibody capture complex, wherein the population of antibody secreting cells comprises the antibody secreting cell that secretes the target antibody, wherein the antibody capture complex comprises a first component of a binding pair linked to an antibody-capture molecule, whereby the first component of the binding pair binds to a second component of the binding pair on the cell surface of the population of antibody secreting cells, and whereby the antibody-capture molecule captures the target antibody secreted by the antibody secreting cell; and contacting the population of the antibody secreting cells with an antigen, whereby the target antibody secreted by the antibody secreting cell and captured by the antibody capture complex binds the antigen. In some embodiments, the method further comprises, after contacting the population of antibody secreting cells with an antibody capture complex, contacting the population of antibody secreting cells with a secondary anti-Ig antibody. The step of contacting with a secondary anti-Ig antibody can be performed before, with, or after the step of contacting the population of antibody secreting cells with an antigen.
In some embodiments, after the population of antibody secreting cells is contacted with an antigen, the method may further comprise sorting the population of antibody secreting cells to collect a pool of antibody secreting cells, wherein the antibody secreting cells in the pool each secrete an antibody that is captured by the antibody capture molecule and is bound by the antigen, wherein the collected pool of antibody secreting cells comprises the antigen secreting cell that secretes the target antibody; and in some such embodiments, the method may further comprise separating the collected pool of antibody secreting cells into single cells and isolating the antigen secreting cell that secretes the target antibody.
In some embodiments, the antigen is a barcoded antigen. In some embodiments, the antigen comprises an allergen. In some embodiments, the barcoded antigen comprises a barcode nucleic acid molecule. In some embodiments, a portion of the nucleotide sequence of the barcode nucleic acid molecule is unique to the antigen. In some embodiments, a portion of the barcode nucleic acid molecule comprises a sequencing primer. In some embodiments, the sequencing primer is upstream of the portion of the nucleotide sequence of the barcode nucleic acid molecule that is unique to the antigen. In some embodiments, a portion of the barcode nucleic acid molecule is complementary to a template switch oligonucleotide (TSO). In some embodiments, the portion of the nucleotide sequence of the barcode nucleic acid molecule is unique to the antigen, is upstream of the portion of the barcode nucleic acid molecule, and is complementary to the ISO. In some embodiments, the 3′ terminus of the barcode nucleic acid molecule comprises three contiguous cytidine or ribocytidine residues. In some embodiments, the barcode nucleic acid molecule comprises DNA. In some embodiments, the barcode nucleic acid molecule comprises RNA.
In some embodiments, the population of antibody secreting cells is contacted with a plurality of barcoded antigens, wherein each barcoded antigen of the plurality of barcoded antigens comprises a unique antigen linked to a unique nucleic acid molecule. In some embodiments, the unique antigen comprises an allergen. In some embodiments, the unique nucleic acid molecule comprises a barcode nucleic acid molecule.
In some embodiments, each barcoded antigen of the plurality of barcoded antigens is detectably labeled. In some embodiments, each barcoded antigen of the plurality of barcoded antigens is labeled with a radioactive compound, a fluorescent compound, or an enzyme. In some embodiments, each barcoded antigen of the plurality of barcoded antigens is labeled with a radioactive compound. In some embodiments, each barcoded antigen of the plurality of barcoded antigens is labeled with a fluorescent compound. In some embodiments, each barcoded antigen of the plurality of barcoded antigens is labeled with an enzyme. In some embodiments, the radioactive compound comprises 3H, 14C, 19F, 35S, 125I, 131I, 111In, or 99Tc. In some embodiments, the radioactive compound comprises 3H. In some embodiments, the radioactive compound comprises 14C. In some embodiments, the radioactive compound comprises 19F. In some embodiments, the radioactive compound comprises 35S. In some embodiments, the radioactive compound comprises 125I. In some embodiments, the radioactive compound comprises 131I. In some embodiments, the radioactive compound comprises 111In. In some embodiments, the radioactive compound comprises 99Tc. In some embodiments, the fluorescent compound comprises fluorescein, fluorescein isothiocyanate, rhodamine, 5-dimethylamine-1-naphthalenesulfonyl chloride, phycoerythrin, or a fluorescent protein. In some embodiments, the fluorescent compound comprises fluorescein. In some embodiments, the fluorescent compound comprises fluorescein isothiocyanate. In some embodiments, the fluorescent compound comprises rhodamine. In some embodiments, the fluorescent compound comprises 5-dimethylamine-1-naphthalenesulfonyl chloride. In some embodiments, the fluorescent compound comprises phycoerythrin. In some embodiments, the fluorescent compound comprises a fluorescent protein. In some embodiments, the enzyme comprises alkaline phosphatase, horseradish peroxidase, luciferase, or glucose oxidase. In some embodiments, the enzyme comprises alkaline phosphatase. In some embodiments, the enzyme comprises horseradish peroxidase. In some embodiments, the enzyme comprises luciferase. In some embodiments, the enzyme comprises glucose oxidase.
In embodiments where a secondary anti-Ig antibody is employed, in some such embodiments, the secondary anti-Ig antibody comprises an anti-IgM antibody, an anti-IgG antibody, an anti-IgA antibody, and/or an anti-IgE antibody. In some embodiments, the secondary anti-Ig antibody comprises an anti-IgM antibody. In some embodiments, the secondary anti-Ig antibody comprises an anti-IgG antibody. In some embodiments, the secondary anti-Ig antibody comprises an anti-IgA antibody. In some embodiments, the secondary anti-Ig antibody comprises an anti-IgE antibody.
In some embodiments, the secondary anti-Ig antibody is detectably labeled. In some embodiments, the secondary anti-Ig antibody is labeled with a radioactive compound, a fluorescent compound, or an enzyme. In some embodiments, the secondary anti-Ig antibody is labeled with a radioactive compound. In some embodiments, the secondary anti-Ig antibody is labeled with a fluorescent compound. In some embodiments, the secondary anti-Ig antibody is labeled with an enzyme. In some embodiments, the radioactive compound comprises 3H, 14C, 19F, 35S, 125I, 131I, 111In, or 99Tc. In some embodiments, the radioactive compound comprises 3H. In some embodiments, the radioactive compound comprises 14C. In some embodiments, the radioactive compound comprises 19F. In some embodiments, the radioactive compound comprises 35S. In some embodiments, the radioactive compound comprises 125I. In some embodiments, the radioactive compound comprises 131I. In some embodiments, the radioactive compound comprises 111In. In some embodiments, the radioactive compound comprises 99Tc. In some embodiments, the fluorescent compound comprises fluorescein, fluorescein isothiocyanate, rhodamine, 5-dimethylamine-1-naphthalenesulfonyl chloride, phycoerythrin, or a fluorescent protein. In some embodiments, the fluorescent compound comprises fluorescein. In some embodiments, the fluorescent compound comprises fluorescein isothiocyanate. In some embodiments, the fluorescent compound comprises rhodamine. In some embodiments, the fluorescent compound comprises 5-dimethylamine-1-naphthalenesulfonyl chloride. In some embodiments, the fluorescent compound comprises phycoerythrin. In some embodiments, the fluorescent compound comprises a fluorescent protein. In some embodiments, the enzyme comprises alkaline phosphatase, horseradish peroxidase, luciferase, or glucose oxidase. In some embodiments, the enzyme comprises alkaline phosphatase. In some embodiments, the enzyme comprises horseradish peroxidase. In some embodiments, the enzyme comprises luciferase. In some embodiments, the enzyme comprises glucose oxidase.
In some embodiments, the population of antibody secreting cells is obtained by enriching a population of cells obtained from a human for immune cells. In some embodiments, the population of cells obtained from the human is enriched for plasma cells or plasmablasts.
In some embodiments, the population of antibody secreting cells is obtained from a lymph node, lung, bone marrow, and/or blood of a human. In some embodiments, the population of antibody secreting cells is obtained from a lymph node. In some embodiments, the population of antibody secreting cells is obtained from a lung. In some embodiments, the population of antibody secreting cells is obtained from bone marrow. In some embodiments, the population of antibody secreting cells is obtained from blood.
In some embodiments, the antigen and/or the secondary anti-Ig antibody are/is detected. In some embodiments, the antibody secreting cells are sorted to collect a pool of antibody secreting cells that are bound by the antigen and/or by the secondary anti-Ig antibody, wherein the collected pool of antibody secreting cells comprises the antibody secreting cell that secretes the target antibody.
In some embodiments, the antibody secreting cells are contacted with an Fc block prior to contacting the population of antibody secreting cells with the second component of the binding pair.
The present disclosure also provides methods of capturing an IgE antibody secreted by an antibody secreting cell, wherein the IgE antibody is directed to an allergen, the method comprising: contacting a population of antibody secreting cells with NHS-biotin to allow biotin to bind to the cell surface, wherein the population of antibody secreting cells comprises the antibody secreting cell that secretes the IgE antibody; contacting the population of antibody secreting cells with an antibody capture complex, wherein the antibody capture complex comprises streptavidin linked to an ectodomain of FcεRIa, and whereby the antibody-capture molecule binds to the IgE antibody secreted by the antibody secreting cell; and contacting the population of antibody secreting cells with an antigen, wherein the antigen is an antigenic portion or a mixture of a plurality of antigenic portions of the allergen, whereby the IgE antibody secreted by the antibody secreting cell and captured by the antibody capture complex binds to the antigen. In some embodiments, the antigen comprises a plurality of barcoded antigens, wherein each of the plurality of barcoded antigens is a different antigenic portion of the allergen. In some embodiments, the method further comprises sorting the population of antibody secreting cells to collect a pool of antibody secreting cells, wherein the antibody secreting cells in the pool each secrete an IgE antibody that is captured by the antibody capture complex and is bound by the antigen, wherein the collected pool of antibody secreting cells comprises the antigen secreting cell that secretes the IgE antibody.
In some embodiments, the method further comprises contacting the population of antibody secreting cells with an anti-IgE antibody to allow the IgE antibody secreted by the antibody secreting cell and captured by the antibody capture complex to bind to the anti-IgE antibody. In some embodiments, the method may further comprise sorting the population of antibody secreting cells to collect a pool of antibody secreting cells, wherein the antibody secreting cells in the pool each secrete an IgE antibody that is captured by the antibody capture complex and is bound by the antigen and the anti-IgE antibody, wherein the collected pool of antibody secreting cells comprises the antigen secreting cell that secretes the IgE antibody.
In some embodiments, the method further comprises separating the collected pool of antibody secreting cells into single cells and isolating the antigen secreting cell that secretes the IgE antibody.
A population of antibody secreting cells may comprise a plurality of antibody secreting cells each secreting an antibody that is captured by the antibody capture complex, wherein the plurality of antibody secreting cells includes the antibody secreting cell that secretes the target antibody. Some of the antibodies secreted by the plurality of antibody secreting cells bind an antigen to which the target antibody binds, although the antibodies may have varying affinities to the antigen. An antigen chase can be employed to obtain a cell population enriched in antibody secreting cells that secrete antibodies having high affinity for the antigen, which allows for isolation of an antibody secreting cell that secretes a target antibody having high affinity. Therefore, in some embodiments of the methods disclosed herein, the step of contacting the population of antibody secreting cells with an antigen includes an antigen chase. In these embodiments, as an initial binding step, the population of antibody secreting cells is contacted with a first labeled form of the antigen to allow the antigen to bind to antibodies including the target antibody captured at the surface of antibody secreting cells and form an antigen-antibody complex, followed by a “chase” step where the cells are contacted with one of several forms of the antigen: (i) an unlabeled form of the antigen (“cold chase”), (ii) a second labeled form of the antigen (“hot chase”), or a combination of an unlabeled form of the antigen and a second labeled form of the antigen (“combination chase”). The cells that remain bound to the first labeled form of the antigen after the chase represent cells secreting antibodies with high binding affinity. Accordingly, an antigen chase permits selection among cells secreting antibodies with different affinities to enrich for cells secreting antibodies with high affinities and subsequent isolation of an antibody secreting cell that secretes a target antibody of high affinity.
The term “enriching” means increasing the frequency or percentage of desired cells in a cell population, e.g., increasing the percentage of antibody secreting cells secreting high affinity antibodies within an antibody secreting cell population containing cells secreting antibodies having various affinities (e.g., high affinity, medium affinity, and low affinity). Thus, an antibody secreting cell population enriched in cells secreting high affinity antibodies encompasses a cell population having a higher frequency and/or higher percentage of antibody secreting cells secreting high affinity antibodies as a result of an enrichment process. In the present context, the enrichment process is a process that includes an antigen chase, thereby selecting cells that secrete high affinity antibodies to an antigen from a population of cells that secrete antibodies of various affinities to the antigen, and separating cells that secrete high affinity antibodies from cells that secrete antibodies not of high affinity.
The cell population obtained as a result of a chase is enriched in antibody-secreting cells secreting antibodies with high binding affinity to an antigen of interest. In other words, the enriched population of cells contains a greater percentage of cells that secretes an antibody that binds to the antigen with high binding affinity, as compared to a cell population before or without a chase. In some embodiments, at least 40% of the cells collected secrete a high affinity antibody, e.g., antibody having a KD from 0.1 pM to 25 nM. In some embodiments, the enriched cell population may be a population having at least 50% of cells within the population secreting an antibody that binds to the antigen of interest with high binding affinity, e.g., antibody having a KD from 0.1 pM to 25 nM. In some embodiments, the enriched cell population may be a population having at least 60% of cells within the population secreting an antibody that binds to the antigen of interest with high binding affinity, e.g., antibody having a KD from 0.1 pM to 25 nM. In some embodiments, the enriched cell population may be a population having at least 70% of cells within the population secreting an antibody that binds to the antigen of interest with high binding affinity, e.g., antibody having a KD from 0.1 pM to 25 nM. In some embodiments, the enriched cell population may be a population having at least 80% of cells within the population secreting an antibody that binds to the antigen of interest with high binding affinity, e.g., antibody having a KD from 0.1 pM to 25 nM. In some embodiments, the enriched cell population may be a population having at least 90% of cells within the population secreting an antibody that binds to the antigen of interest with high binding affinity, e.g., antibody having a KD from 0.1 pM to 25 nM. In some embodiments, the enriched cell population may be a population having at least 95% of cells within the population secreting an antibody that binds to the antigen of interest with high binding affinity, e.g., antibody having a KD from 0.1 pM to 25 nM. In some embodiments, the frequency of cells secreting high affinity antibodies (e.g., antibody having a KD from 0.1 pM to 25 nM) in the cell population after a chase is increased by at least 30% as compared to the frequency in the cell population before or without the chase. In some embodiments, the frequency of cells secreting high affinity antibodies (e.g., antibody having a KD from 0.1 pM to 25 nM) in the cell population after a chase is increased by at least 40% as compared to the frequency in the cell population before or without the chase. In some embodiments, the frequency of cells secreting high affinity antibodies (e.g., antibody having a KD from 0.1 pM to 25 nM) in the cell population after a chase is increased by at least 50% as compared to the frequency in the cell population before or without the chase. In some embodiments, the frequency of cells secreting high affinity antibodies (e.g., antibody having a KD from 0.1 pM to 25 nM) in the cell population after a chase is increased by at least 75% as compared to the frequency in the cell population before or without the chase. In some embodiments, the frequency of cells secreting high affinity antibodies (e.g., antibody having a KD from 0.1 pM to 25 nM) in the cell population after a chase is increased by at least 100% as compared to the frequency in the cell population before or without the chase. In some embodiments, the frequency of cells secreting high affinity antibodies (e.g., antibody having a KD of 0.1 pM to 25 nM) in the cell population after a chase is increased by at least 200% as compared to the frequency in the cell population before or without the chase. In some embodiments, the frequency of cells secreting high affinity antibodies having a KD of less than 1 nM (e.g., antibody having a KD from 0.1 pM to 1 nM) in the cell population after a chase is increased by at least 40% as compared to the frequency in the cell population before or without the chase. In some embodiments, the frequency of cells secreting high affinity antibodies having a KD of less than 1 nM (e.g., antibody having a KD from 0.1 pM to 1 nM) in the cell population after a chase is increased by at least 50% as compared to the frequency in the cell population before or without the chase. In some embodiments, the frequency of cells secreting high affinity antibodies having a KD of less than 1 nM (e.g., antibody having a KD from 0.1 pM to 1 nM) in the cell population after a chase is increased by at least 75% as compared to the frequency in the cell population before or without the chase. In some embodiments, the frequency of cells secreting high affinity antibodies having a KD of less than 1 nM (e.g., antibody having a KD from 0.1 pM to 1 nM) in the cell population after a chase is increased by at least 100% as compared to the frequency in the cell population before or without the chase. In some embodiments, the frequency of cells secreting high affinity antibodies having a KD of less than 1 nM (e.g., antibody having a KD from 0.1 pM to 1 nM) in the cell population after a chase is increased by at least 200% as compared to the frequency in the cell population before or without the chase. In some embodiments, the frequency of cells secreting high affinity antibodies having a KD of less than 0.1 nM (e.g., antibody having a KD from 0.1 pM to 0.1 nM) in the cell population after a chase is increased by at least 40% as compared to the frequency in the cell population before or without the chase. In some embodiments, the frequency of cells secreting g high affinity antibodies having a KD of less than 0.1 nM (e.g., antibody having a KD from 0.1 pM to 0.1 nM) in the cell population after a chase is increased by at least 50% as compared to the frequency in the cell population before or without the chase. In some embodiments, the frequency of cells secreting high affinity antibodies having a KD of less than 0.1 nM (e.g., antibody having a KD from 0.1 pM to 0.1 nM) in the cell population after a chase is increased by at least 75% as compared to the frequency in the cell population before or without the chase. In some embodiments, the frequency of cells secreting high affinity antibodies having a KD of less than 0.1 nM (e.g., antibody having a KD from 0.1 pM to 0.1 nM) in the cell population after a chase is increased by at least 100% as compared to the frequency in the cell population before or without the chase. In some embodiments, the frequency of cells secreting high affinity antibodies having a KD of less than 0.1 nM (e.g., antibody having a KD from 0.1 pM to 0.1 nM) in the cell population after a chase is increased by at least 200% as compared to the frequency in the cell population before or without the chase.
“Binding affinity,” as that term is known in the art, generally refers to the strength of the sum total of noncovalent interactions between a single binding site of a molecule (e.g., an antibody) and its binding partner (e.g., an antigen). Unless indicated otherwise, as used herein, “binding affinity” refers to intrinsic binding affinity which reflects a 1:1 interaction between members of a binding pair (e.g., antibody and antigen). The affinity of a molecule for its binding partner can generally be represented by the dissociation equilibrium constant (KD or KD). There is an inverse relationship between KD (molar) value and binding affinity, therefore the smaller the KD value (M), the higher the affinity. Thus “higher affinity” refers to antibodies that generally bind antigen stronger and/or faster and/or remain bound longer. Generally, a lower concentration (M) of antigen is needed to achieve the desired effect due to its stronger binding interaction.
The term “kd” (sec−1 or 1/s) refers to the dissociation rate constant of a particular antibody-antigen interaction, or the dissociation rate constant of an antibody, Ig, antibody-binding fragment, or molecular interaction. This value is also referred to as the koff value.
The term “ka” (M−1×sec−1 or 1/M) refers to the association rate constant of a particular antibody-antigen interaction, or the association rate constant of an antibody, Ig, antibody-binding fragment, or molecular interaction.
The term “KD” or “KD” (M) refers to the equilibrium dissociation constant of a particular antibody-antigen interaction, or the equilibrium dissociation constant of an antibody, Ig, antibody-binding fragment, or molecular interaction. The equilibrium dissociation constant is obtained by dividing the ka with the kd.
A variety of methods of measuring binding affinity are known in the art, any of which can be used for purposes of the present invention. Binding affinities obtained using the method are typically in the range of about 0.1 pM to about 25 nM as determined by surface plasmon resonance. In some embodiments, binding affinities are less than about 10 nM as determined by surface plasmon resonance.
The term “high affinity” antibody refers to those antibodies having a binding affinity, expressed as KD, of 25 nM or less, e.g., having a numerical value of about 0.1 pM to about 25 nM. To this end, high affinity antibodies may have a measured KD about 25×10−9 M (25 nM) or less, about 10×10−9 M (10 nM) or less, about 1×10−9 M (1 nM) or less, about 1×10−10 M (0.1 nM) or less, about 0.5×10−10 M (0.05 nM) or less, about 0.05×10−10 M (5 pM) or less, about 1 pM or less, or about 0.5 pM or less, as measured by surface plasmon resonance, e.g., BIACORE™ or solution-affinity ELISA. Those of skill in the art will recognize that values for KD of antibodies may be represented numerically either as nE−z, or as n×10−z, for example, 3.2E−12 is equivalent to 3.2×10−12 and indicates a KD of 3.2 picomolar (pM). In some embodiments, the high affinity antibodies have a measured KD in a range of from about 0.1 pM to about 25 nM. In some embodiments, the high affinity antibodies have a measured KD in a range of from about 0.1 pM to about 20 nM. In some embodiments, the high affinity antibodies have a measured KD in a range of from about 0.1 pM to about 15 nM. In some embodiments, the high affinity antibodies have a measured KD in a range of from about 0.1 pM to about 10 nM. In some embodiments, the high affinity antibodies have a measured KD in a range of from about 0.1 pM to about 5 nM. In some embodiments, the high affinity antibodies have a measured KD in a range of from about 0.1 pM to about 1 nM. In some embodiments, the high affinity antibodies have a measured KD in a range of from about 0.1 pM to about 0.5 nM. In some embodiments, the high affinity antibodies have a measured KD in a range of from about 0.1 pM to about 0.1 nM. In some embodiments, the high affinity antibodies have a measured KD of less than about 20 nM. In some embodiments, the high affinity antibodies have a measured KD of less than about less than about 15 nM. In some embodiments, the high affinity antibodies have a measured KD of less than about 10 nM. In some embodiments, the high affinity antibodies have a measured KD of less than about 5 nM. In some embodiments, the high affinity antibodies have a measured KD of less than about 1 nM. In some embodiments, the high affinity antibodies have a measured KD of less than about 0.1 nM. In some embodiments, the high affinity antibodies have a measured KD of less than about 0.5 nM. In some embodiments, the high affinity antibodies have a measured KD of less than about 0.01 nM. In some embodiments, the high affinity antibodies have a measured KD of less than about 0.001 nM (or 1 pM). In some embodiments, the high affinity antibodies have a measured KD of less than about 0.5 pM.
In some embodiments, the antigen is a protein that is present in a monomeric form. Examples of proteins that exist in monomers include interleukin molecules, such as IL-13. In some embodiments, the antigen is a protein that is present in a multimeric form, including homomers and heteromers. In some embodiments, the antigen is a protein that is present in both monomeric and multimeric forms, in which case a mixture of protein monomers and multimers can be used in the method described herein.
Whether the antigen is a protein that is present in a monomeric form, multimeric form, or a mixture there, the antigen may be employed in the methods described herein in a monovalent form or a multivalent form. The terms “monovalent” and “multivalent” are used to refer to the number of units of antigen being presented and to differentiate from the antigen itself being a protein in a monomer form, a multimer form or a mixture thereof. Thus, a monovalent form of an antigen refers to a single unit form of the antigen, where the antigen itself may be a protein in a monomeric form, a multimeric form or a mixture thereof. A multivalent form of an antigen refers to multiple units of the antigen being presented, typically by way of a multivalent molecule to which the antigen is bound or linked. A multivalent molecule can be a dimer, trimer, tetramer, pentamer, hexamer, and the like, or a mixture thereof. In some embodiments, the multivalent molecule is a streptavidin multimer (e.g., tetramer), which can be complexed with biotin which is then linked to the antigen, thereby providing a multivalent (e.g., tetravalent form) of the antigen. In some embodiments, a streptavidin multimer includes tetramer and may additionally include trimer and/or dimer. In some embodiments, a streptavidin multimer is conjugated with a fluorophore such as phycoerythrin. In some embodiments, the multivalent molecule is a dimer of an immunoglobulin Fc fragment, to which the antigen can be linked to provide a bivalent form of the antigen. In some embodiments, the multivalent molecule is a trimer of a trimerization molecule, such as foldon, to which the antigen can be linked to provide a trivalent form of the antigen.
In some embodiments, the step of contacting the population of antibody secreting cells with an antigen comprises: (a) contacting the population of antibody-secreting cells with a first labeled form of the antigen to allow the antigen to bind to antibodies including the target antibody captured on the cell surface, wherein the antigen of the first labeled form is conjugated to a first detectable label; (b) washing the cells to remove unbound antigen; (c) contacting the cells with either (i) an unlabeled form of the antigen, (ii) a second labeled form of the antigen, or (iii) the unlabeled form of the antigen and the second labeled form of the antigen; (d) washing the cells to remove unbound antigen; (e) collecting a pool of antibody secreting cells remaining bound to the first labeled form of the antigen, wherein the collected pool of antibody secreting cells comprises the antibody secreting cell that secretes the target antibody, wherein the target antibody secreted by the antibody secreting cell and captured by the antibody capture complex remains bound to the first labeled form of the antigen.
In some embodiments, the first labeled form of the antigen is at a concentration between 0.001 nM and 1 uM. In some embodiments, the first labeled form of the antigen is at a concentration between 0.01 nM and 100 nM. In some embodiments, the first labeled form of the antigen is at a concentration between 0.05 nM to 10 nM. In some embodiments, the first labeled form of the antigen is at a concentration between 0.05 nM to 9 nM, 0.05 nM to 8 nM, 0.05 nM to 7 nM, 0.05 nM to 6 nM, 0.05 nM to 5 nM, 0.05 nM to 4 nM, 0.05 nM to 3 nM, 0.05 nM to 2 nM, or 0.05 nM to 1 nM. In some embodiments, the first labeled form of the antigen is at a concentration between 0.1 nM to 7.5 nM. In some embodiments, the first labeled form of the antigen is at a concentration between 0.1 nM to 7 nM, 0.1 nM to 6 nM, 0.1 nM to 5 nM, 0.1 nM to 4 nM, 0.1 nM to 3 nM, 0.1 nM to 2 nM, or 0.1 nM to 1 nM. In some embodiments, the first labeled form of the antigen is at a concentration between 0.2 nM to 7.5 nM. In some embodiments, the first labeled form of the antigen is at a concentration between 0.2 nM to 7 nM, 0.2 nM to 6 nM, 0.2 nM to 5 nM, 0.2 nM to 4 nM, 0.2 nM to 3 nM, 0.2 nM to 2 nM, 0.2 nM to 1 nM, 0.3 nM to 7 nM, 0.3 nM to 6 nM, 0.3 nM to 5 nM, 0.3 nM to 4 nM, 0.3 nM to 3 nM, 0.3 nM to 2 nM, 0.3 nM to 1 nM, 0.5 nM to 7 nM, 0.5 nM to 6 nM, 0.5 nM to 5 nM, 0.5 nM to 4 nM, 0.5 nM to 3 nM, 0.5 nM to 2 nM, 0.5 nM to 1 nM. In some embodiments, the first labeled form of the antigen is at a concentration between 1.0 nM to 10 nM, 1.0 nM to 9 nM, 1.0 nM to 8.0 nM, 1.0 nM to 7 nM, 1.0 nM to 6 nM, 1.0 nM to 5 nM, 1.0 nM to 4 nM, 1.0 nM to 3 nM, 1.0 nM to 2 nM, 2.0 nM to 10.0 nM, or 5.0 nM to 10.0 nM. In specific embodiments, the antibody-secreting cells can be contacted with a first labeled form of the antigen where the first labeled form of the antigen is at a concentration of 0.2 nM. In specific embodiments, the antibody-secreting cells can be contacted with a first labeled form of the antigen where the first labeled form of the antigen is at a concentration of 5.0 nM. In specific embodiments, the antibody-secreting cells can be contacted with a first labeled form of the antigen where the first labeled form of the antigen is at a concentration of 7.5 nM. In specific embodiments, the antibody-secreting cells can be contacted with a first labeled form of the antigen where the first labeled form of the antigen is at a concentration of 10 nM. In specific embodiments, the antibody-secreting cells can be contacted with a first labeled form of the antigen where the first labeled form of the antigen is at a concentration of 0.1 nM, 0.2 nM, 0.3 nM, 0.4 nM, 0.5 nM, 0.6 nM, 0.7 nM, 0.8 nM, 0.9 nM, 1.0 nM, 1.5 nM, 2.0 nM, 2.5 nM, 3.0 nM, 3.5 nM, 4.0 nM, 4.5 nM, 5.0 nM, 5.5 nM, 6.0 nM, 6.5 nM, 7.0 nM, 8.0 nM, 8.5 nM, 9.0 nM, 9.5 nM, or greater.
In some embodiments, the contacting of the antibody secreting cells with a first labeled form of the antigen occurs from about 5 to about 60 minutes, e.g., about 20 minutes, about 30 minutes, about 40 minutes, or about 50 minutes.
In some embodiments, the first labeled form of antigen is a monovalent form of the antigen. In some embodiments, the first labeled form of antigen is a multivalent form of the antigen. In some embodiments, the first labeled form of antigen is a mixture of monovalent and multivalent forms of the antigen. Whether a monovalent form, a multivalent form or a mixture thereof, the antigen itself can be a protein that is a monomer, multimer, or a mixture of monomer and multimer.
In some embodiments, the first labeled form of the antigen is the antigen conjugated to a first detectable label. The antigen can be labeled with small molecules, radioisotopes, enzymatic proteins and fluorescent dyes. In some embodiments, the detectable label is a small molecule. Detectable small molecule labels allow for easy labeling of proteins and can be used in a number of regularly deployed detection assays known in the art.
In some embodiments, the detectable label is an enzyme reporter. Enzyme labels are larger than biotin, however, they rarely disrupt antibody function. Commonly used enzyme labels are horseradish peroxidase (HRP), alkaline phosphatase (AP), glucose oxidase and β-galactosidase. To use enzyme-labeled antibodies, samples are incubated with an enzyme-specific substrate that is catalyzed by the enzyme to produce a colored product (chromogenic assays) or light (chemiluminescent assays). Each enzyme has a set of substrates and detection methods that can be employed. For example, HRP can be reacted with diaminobenzidine to produce a brown-colored product or with luminol to produce light. In contrast, AP can be reacted with para-Nitrophenylphosphate (pNPP) to produce a yellow-colored product detected by a spectrophotometer or with 5-bromo-4-chloro-3-indolyl phosphate (BCIP) and nitroblue tetrazolium (NBT) to produce a purple-colored precipitate.
In some embodiments, the detectable label is a fluorescent label. Fluorescent labels are directly conjugated to the antibody, no enzyme/substrate or binding interactions are required for detection. Therefore, the amount of fluorescent signal detected is directly proportional to the amount of target protein in the sample. Fluorescent tags can be covalently attached to antibodies through primary amines or thiol.
After incubation of the population of antibody-secreting cells with a first labeled form of the antigen (the initial binding step), any unbound antigen can be removed from the primary antibody-producing cells. In some embodiments, the unbound antigen is removed through washing. As is known in the art, washing is a technique where a wash buffer is used to remove unwanted components including unbound antigen. Wash buffers are known in the art. In some embodiments, the wash buffer is a phosphate buffered saline (PBS) based wash buffer. In some embodiments, the wash buffer is a Tris buffered saline (TBS) wash buffer. In some embodiments, the wash buffer comprises a detergent. In some embodiments, the detergent is Tween-20. The cells are washed with wash buffer for an allotted time in order to remove unbound antigen. This allotted amount of time will be an amount of time sufficient to remove unbound antigen. In some embodiments, this allotted time can be from about 10 minutes to about 60 minutes to remove unbound antigen; multiple washes that total from 10 to 60 minutes may be used, e.g., 3 washes of 10 minutes or one 30-minute wash; 2-4 washes of 5-15 minutes each, etc. After washing and aspirating the supernatant comprising the wash buffer and unbound antigen, the pellet comprising cells bound with antigen can be used in subsequent steps. In some embodiments, the pellet comprising the bound antigen can be resuspended in a buffer and used in subsequent steps. In some embodiments, the buffer used to resuspend the pellet can be the same wash buffer. In some embodiments, the buffer used to resuspend the pellet can be a different buffer than the wash buffer.
After contacting a population of antibody secreting cells with the first labeled form of antigen (initial binding/contacting step) and once the unbound first labeled form of antigen is removed, the cells are subjected to antigen chase, i.e., the cells are contacted again, or “chased,” with the antigen to selectively enrich for cells secreting antibodies with high affinities to the antigen. This chase can be performed using any of the several forms of the antigen: (i) an unlabeled form of the antigen (“cold” chase), (ii) a second labeled form of the antigen (“hot” chase); or (iii) an unlabeled form of the antigen and a second labeled form of the antigen (a “combination chase”). The chase allows the chase antigen to bind to the antibody initially bound by the first labeled form of the antigen, thereby chasing the first labeled form of the antigen off the antibody, unless the antibody has high affinity for the antigen and remains bound to the first labeled form of the antigen after the chase.
In some embodiments, the chase is performed using an unlabeled form of the antigen (cold chase). In some embodiments, the unlabeled form of the antigen is a monovalent form of the antigen—that is, while the antigen itself can be a protein in a monomeric form, a multimeric form, or a mixture of monomeric and multimeric forms, a monovalent form of the antigen is the antigen itself without further, secondary multimerization. In some embodiments, the unlabeled form of the antigen is a multivalent form of the antigen, where the antigen itself can be a protein in a monomeric form, a multimeric form, or a mixture of monomeric and multimeric forms. In some embodiments, the unlabeled form of the antigen is a mixture of a monovalent form and a multivalent form of the antigen. In embodiments where a multivalent form of the antigen is used, such form can be provided by a multivalent molecule to which the antigen is bound or linked. In some embodiments, the multivalent molecule is a streptavidin multimer (e.g., tetramer), which can be complexed with biotin which is then linked to the antigen, thereby providing a multivalent (e.g., tetravalent) form of the antigen. In some embodiments, a streptavidin multimer may include trimer and/or dimer in addition to tetramer. In some embodiments, the multivalent molecule is a dimer of an immunoglobulin Fc fragment, to which the antigen can be linked to provide a bivalent form of the antigen. In some embodiments, the multivalent molecule is a trimer of a trimerization molecule, such as foldon, to which the antigen can be linked to provide a trivalent form of the antigen.
In some embodiments, the chase is performed using a second labeled form of the antigen (hot chase). In such embodiments, after the initial binding and washing steps, the antibody secreting cells are chased with a second labeled form of the antigen. The second labeled form of the antigen has a label that provides a different detectable signal than the label on the first labeled form of the antigen. Suitable choices of the label have been described herein, as long as the label on the second labeled form of the antigen is different from the label on the first labeled form of antigen. Such labels include small molecules, radioisotopes, enzymatic proteins and fluorescent dyes. In some embodiments, the first label is AlexaFluor647, and the second label is phycoerythrin.
In some embodiments, the second labeled form of the antigen is a monovalent form of the antigen. In some embodiments, the second labeled form of the antigen is a multivalent form of the antigen. In some embodiments, the second labeled form of the antigen comprises a mixture of a monovalent and a multivalent form of the antigen. In embodiments where a multivalent form of the antigen is used, such form can be provided by a multivalent molecule to which the antigen is bound or linked. In some embodiments, the multivalent molecule is a streptavidin multimer (e.g., tetramer), which can be complexed with biotin which is then linked to the antigen, thereby providing a multivalent (e.g., tetravalent) form of the antigen. In some embodiments, a streptavidin multimer may include trimer and/or dimer in addition to tetramer. In some embodiments, a streptavidin multimer is conjugated with a fluorophore such as phycoerythrin. In some embodiments, the multivalent molecule is a dimer of an immunoglobulin Fc fragment, to which the antigen can be linked to provide a bivalent form of the antigen. In some embodiments, the multivalent molecule is a trimer of a trimerization molecule, such as foldon, to which the antigen can be linked to provide a trivalent form of the antigen.
The first labeled form of the antigen and the second labeled form of the antigen can be the same or different valent form of the antigen but must have labels that emit different detectable signals from each other. In some embodiments, the first labeled form of the antigen is a monovalent form of the antigen and the second labeled form of antigen is also a monovalent form. In some embodiments, the first labeled form of the antigen is a monovalent form of the antigen whereas the second labeled form of the antigen is a multivalent form.
In some embodiments, the chase is performed with an unlabeled form of an antigen (cold) and a second labeled form of the antigen (hot), also referred herein as a combination chase. In such embodiments, after the initial binding and washing steps, the antibody-secreting cells are chased with an unlabeled form of the antigen and a second labeled form of the antigen. The two forms of chase antigen: the unlabeled form of the antigen (“cold chase antigen”) and the second labeled form of the antigen (“hot chase antigen”) can be brought into contact with the cells at the same time or sequentially (e.g., with the cold chase antigen being added first, followed by the hot chase antigen, or vice versa). In some embodiments, the unlabeled form of the antigen is a monovalent form. In some embodiments, the unlabeled form of the antigen is a multivalent form. In some embodiments, the unlabeled form of the antigen is a mixture of monovalent form and multivalent form. In some embodiments, the second labeled form of the antigen is a monovalent form. In some embodiments, the second labeled form of the antigen is a multivalent form. In some embodiments, the second labeled form of the antigen comprises a mixture of a monovalent form and a multivalent form. In embodiments where a multivalent form of the antigen is used in a combination chase, such form can be provided by a multivalent molecule to which the antigen is bound or linked. In some embodiments, the multivalent molecule is a streptavidin multimer (e.g., tetramer), which can be complexed with biotin which is then linked to the antigen, thereby providing a multivalent (e.g., tetravalent) form of the antigen. In some embodiments, a streptavidin multimer may include trimer and/or dimer in addition to tetramer. In some embodiments, the multivalent molecule is a dimer of an immunoglobulin Fc fragment, to which the antigen can be linked to provide a bivalent form of the antigen. In some embodiments, the multivalent molecule is a trimer of a trimerization molecule, such as foldon, to which the antigen can be linked to provide a trivalent form of the antigen.
For any format of the chase, the chase antigen concentration used is in excess as compared to the concentration of the first labeled form of the antigen, irrespective of the form of antigen used for the chase (i.e., unlabeled form, a second labeled form, or an unlabeled form and a second labeled form). In embodiments where an unlabeled form of the antigen is used (in a cold chase or in a combination chase), the antigen in the unlabeled form is at least 2 fold, i.e., 2 fold to up to, e.g., 2500 fold, in molar ratio relative to the first labeled form of the antigen. In some embodiments, the antigen in the unlabeled form is 2-fold in molar ratio relative to the first labeled form of the antigen. In some embodiments, the antigen in the unlabeled form is 3-fold in molar ratio relative to the first labeled form of the antigen. In some embodiments, the antigen in the unlabeled form is 4-fold in molar ratio relative to the first labeled form of the antigen. In some embodiments, the antigen in the unlabeled form is 5-fold in molar ratio relative to the first labeled form of the antigen. In some embodiments, the antigen in the unlabeled form is 6-fold, 7-fold, 8-fold, or 9-fold in molar ratio relative to the first labeled form of the antigen. In some embodiments, the antigen in the unlabeled form is 10-fold, 15-fold, 20-fold, or 25-fold in molar ratio relative to the first labeled form of the antigen. In some embodiments, the antigen in the unlabeled form is 30-fold, 40-fold, 50-fold, 60-fold, 70-fold, 80-fold, 90-fold, 100-fold, 150-fold, or greater in molar ratio relative to the first labeled form of the antigen. In some embodiments, depending on the concentration of the first labeled form of the antigen, the unlabeled form of the antigen may be at a concentration between 0.4 nM to 1 uM, or 10 to 600 nM. In some embodiments, depending on the concentration of the first labeled form of the antigen, the unlabeled form of the antigen is at a concentration between 10 nM to 600 nM, 10 nM to 500 nM, 10 nM to 400 nM, 10 nM to 300 nM, 10 nM to 200 nM, 10 nM to 150 nM, 10 nM to 100 nM, 10 nM to 75 nM, 10 nM to 65 nM, 10 nM to 50 nM, 10 nM to 40 nM, 10 nM to 30 nM, 10 nM to 25 nM, or 10 nM to 20 nM. In embodiments where a second labeled form of the antigen is used (in a hot chase or a combination chase), the antigen in the second labeled form is at least 2 fold, i.e., 2 fold to up to, e.g., 2500 fold, in molar ratio relative to the first labeled form of the antigen. In some embodiments, the antigen in the second labeled form is 2-fold in molar ratio relative to the first labeled form of the antigen. In some embodiments, the antigen in the second labeled form is 3-fold in molar ratio relative to the first labeled form of the antigen. In some embodiments, the antigen in the second labeled form is 4-fold in molar ratio relative to the first labeled form of the antigen. In some embodiments, the antigen in the second labeled form is 5-fold in molar ratio relative to the first labeled form of the antigen. In some embodiments, the antigen in the second labeled form is 6-fold, 7-fold, 8-fold, or 9-fold in molar ratio relative to the first labeled form of the antigen. In some embodiments, the antigen in the second labeled form is 10-fold, 15-fold, 20-fold, or 25-fold in molar ratio relative to the first labeled form of the antigen. In some embodiments, the antigen in the second labeled form is 30-fold, 40-fold, 50-fold, 60-fold, 70-fold, 80-fold, 90-fold, 100-fold, 150-fold, or greater in molar ratio relative to the first labeled form of the antigen. In some embodiments, depending on the concentration of the first labeled form of the antigen, the second labeled form of the antigen may be at a concentration between 0.4 nM to 1 uM, or 10 nM to 600 nM. In some embodiments, depending on the concentration of the first labeled form of the antigen, the second labeled form of the antigen may be at a concentration between 10 nM to 600 nM, 10 nM to 500 nM, 10 nM to 400 nM, 10 nM to 300 nM, 10 nM to 200 nM, 10 nM to 150 nM, 10 nM to 100 nM, 10 nM to 75 nM, 10 nM to 65 nM, 10 nM to 50 nM, 10 nM to 40 nM, 10 nM to 30 nM, 10 nM to 25 nM, or 10 nM to 20 nM.
In some embodiments where a combination chase is performed, the cold chase antigen and hot chase antigen can be at the same concentration or at different concentrations.
In some embodiments of a combination chase, the cells are contacted with a cold chase antigen and a hot chase antigen sequentially; and in some such embodiments, a washing step can be included between the two chase antigens. In such embodiments, the cells are washed with wash buffer for an allotted time sufficient to remove unbound antigen. In some embodiments, washing the cells for a period of time of about 10 minutes to about 60 minutes, in one or more washes.
The chase is performed for a period of time sufficient to allow the chase antigen to bind to antibodies. In some embodiments, the chase is performed with an unlabeled form or a second labeled form of the antigen for a time of about 5 to about 60 minutes, e.g., about 10 minutes, about 20 minutes, about 30 minutes, about 40 minutes, about 45 minutes, or about 50 minutes. In some embodiments of a combination chase, the chase is performed with an unlabeled form of the antigen for a time of about 5 to about 60 minutes followed by incubating with a second labeled form of the antigen for a time of about 5 to about 60 minutes. The time of incubation with the unlabeled form of antigen and with the second labeled form of antigen can be the same or different length. As a non-limiting example, the unlabeled form of antigen may contact the cells for about 30 minutes while the second labeled form of the antigen may subsequently contact the cells for about 45 minutes, and vice versa. In some embodiments of a combination chase, the chase is performed with a second labeled form of the antigen for a time of about 5 to about 60 minutes. In some embodiments of a combination chase, the chase is performed with an unlabeled form of the antigen and a second labeled form of the antigen at the same time for a time of about 5 to about 60 minutes.
In some embodiments, the chase is performed more than once. In some embodiments, the cold chase is performed more than once. In some embodiments, the hot chase is performed more than once. In some embodiments, the cold chase is performed once followed by a hot chase performed more than once. In some embodiments, a cold chase is performed more than once followed by a hot chase performed once. In some embodiments, a cold chase is performed more than once followed by a hot chase performed more than once. In some embodiments, a combination chase is performed more than once. In some embodiments, a wash step is included after each chase step. In some embodiments, more than one wash step is included after each chase step, e.g., 2 washes or 3 washes.
After chase has been completed, unbound antigen is again removed through washing and the cells remaining bound to the first labeled form of the antigen are collected. In some embodiments where the first detectable label is a first fluorescent label, fluorescence-activated cell sorting (FACS) can be utilized to collect the cells remaining bound to the first labeled form of the antigen. In some embodiments where the first detectable label is a first fluorescent label, and the second detectable label is a second fluorescent label that differentiates from the first fluorescent label, two-dimensional FACS is used to collect cells that remain bound to the first labeled form of the antigen. In specific embodiments, the first detectable label is A647 and the second detectable label is Phycoerythrin.
A pool of antibody secreting cells can be sorted or separated into single cells. Protocols for single cell isolation by flow cytometry are well-known (Huang, J. et al, 2013, supra). Single cells may be sorted and collected by alternative methods known in the art, including but not limited to manual single cell picking, limited dilution, microfluidics, laser capture microdissection, and Gel Bead Emulsions (GEMs), which are all well-known in the art. See, for example, Rolink et al., J. Exp Med (1996) 183:187-194; Lightwood, D. et al, J. Immunol. Methods (2006) 316(1-2):133-43; Gross et al., Int. J. Mol. Sci. (2015) 16: 16897-16919; and Zheng et al., Nature Communications (2017) 8: 14049. Gel Bead Emulsions (GEMs) are also commercially available (e.g., 10×Chromium System from 10× Genomics, Pleasanton, CA).
Once obtained, single antibody-secreting cells may be propagated by common cell culture techniques for subsequent DNA preparation. Alternatively, antibody genes may be amplified from single antibody-producing cells directly and subsequently cloned into DNA vectors.
A nucleic acid encoding an antibody or a fragment thereof can be isolated from single antibody-secreting cells obtained herein. For example, genes or nucleic acids encoding immunoglobulin variable heavy and variable light chains (i.e., VH, VL, VL can be VK or VA) can be recovered using RT-PCR protocols with nucleic acids isolated from antibody-secreting cells. For example, a nucleic acid encoding an antibody fragment is first reverse-transcribed (RT) to complementary DNA (cDNA). The cDNA is subsequently amplified in PCR reactions using primers specific to antibody gene sequences, e.g., constant regions of an antibody chain. All chains can be amplified using chain-specific primers in multiplex or separately. The amplicons are then sequenced to obtain the nucleic acid sequence encoding the antibody fragment. These RT-PCR protocols are well known and conventional techniques, as described for example, by Wang et al., J. Immunol. Methods (2000) 244:217-225 and described herein.
In some embodiments, the nucleic acid encodes a fragment of an antibody, such as a variable domain, constant domain or combination thereof. In certain embodiments, the nucleic acid isolated from an antibody-producing cell encodes a variable domain of an antibody. In some embodiments, the nucleic acid encodes an antibody heavy chain or a fragment thereof. In other embodiments, the nucleic acid encodes an antibody light chain or a fragment thereof.
Once recovered, antibody-encoding genes or nucleic acids can be cloned into IgG heavy- and light-chain expression vectors and expressed via transfection of host cells. For example, antibody-encoding genes or nucleic acids can be inserted into a replicable vector for further cloning (amplification of the DNA) or for expression (stably or transiently) in cells. Many vectors, particularly expression vectors, are available or can be engineered to comprise appropriate regulatory elements required to modulate expression of an antibody encoding gene or nucleic acid.
An expression vector in the context of the present disclosure can be any suitable vector, including chromosomal, non-chromosomal, and synthetic nucleic acid vectors (a nucleic acid sequence comprising a suitable set of expression control elements) as described herein. Examples of such vectors include derivatives of SV40, bacterial plasmids, phage DNA, baculovirus, yeast plasmids, vectors derived from combinations of plasmids and phage DNA, and viral nucleic acid (RNA or DNA) vectors.
In some embodiments, a nucleic acid molecule is included in a naked DNA or RNA vector, including, for example, a linear expression element (as described in, for instance, Sykes and Johnston, Nat Biotech (1997) 12:355-59), a compacted nucleic acid vector (as described in for instance U.S. Pat. No. 6,077,835), or a plasmid vector such as pBR322 or pUC 19/18. Such nucleic acid vectors and the usage thereof are well known in the art. See, for example, U.S. Pat. Nos. 5,589,466 and 5,973,972.
In certain embodiments, the expression vector can be a vector suitable for expression in a yeast system. Any vector suitable for expression in a yeast system may be employed. Suitable vectors include, for example, vectors comprising constitutive or inducible promoters such as yeast alpha factor, alcohol oxidase and PGH. See, F. Ausubel et al., ed. Current Protocols in Molecular Biology, Greene Publishing and Wiley InterScience New York (1987); and Grant et al., Methods in Enzymol 153, 516-544 (1987).
In some embodiments, an expression vector carrying a nucleic acid isolated from antibody-secreting cell and encoding an antibody or fragment thereof is introduced into a host cell for expression of the antibody or the fragment thereof. Host cells include, e.g., mammalian cells, yeast cell, bacterial cells, or insect cells. In some embodiments, the host cells are cultured under conditions that express the nucleic acid, and the antibody or portion thereof can then be produced and isolated for further use. In some embodiments, host cells comprising one or more of the above nucleic acids are cultured under conditions that express a full-length antibody, and the antibody can then be produced and isolated for further use. In certain embodiments, the host cell comprises a nucleic acid that encodes a variable domain of an antibody, and the cell is cultured under conditions that express the variable domain. In other embodiments, the host cell comprises a nucleic acid that encodes a variable heavy chain (VH) domain of an antibody, and the cell is cultured under conditions that express the VH domain. In another embodiment, the host cell comprises a nucleic acid that encodes a variable light chain (VL) domain of an antibody, and the cell is cultured under conditions that express the VL domain. In specific embodiments, the host cell comprises a nucleic acid that encodes a VH domain of an antibody and nucleic acid that encodes a VL domain of an antibody, and the cell is cultured under conditions that express the VH domain and the VL domain.
In some embodiments, the host cell is a bacterial or yeast cell. In some embodiments, the host cell is a mammalian cell. In other embodiments, the host cell can be, for example, a Chinese hamster ovarian cells (CHO) such as, CHO K1, DXB-11 CHO, Veggie-CHO cells; a COS (e.g., COS-7); a stem cell; retinal cells; a Vero cell; a CV1cell; a kidney cell such as, for example, a HEK293, a 293 EBNA, an MSR 293, an MDCK, aHaK, a BHK21 cell; a HeLa cell; a HepG2 cell; W138; MRC 5; Colo25; HB 8065; HL-60; a Jurkat or Daudi cell; an A431 (epidermal) cell; a CV-1, U937, 3T3 or L-cell; a C127 cell, SP2/0, NS-0 or MMT cell, a tumor cell, and a cell line derived from any of the aforementioned cells. In a particular embodiment, the host cell is a CHO cell. In a specific embodiment, the host cell is a CHO K1 cell.
The present disclosure also provides methods of identifying a region of a gene encoding an antigen-binding fragment of a target antibody, wherein the target antibody is secreted by an antibody secreting cell comprising a modified cell surface, and wherein the target antibody is subsequently captured on the modified cell surface, the method comprising: a) providing an antibody secreting cell comprising a modified cell surface, wherein the cell secretes a target antibody wherein the target antibody is subsequently captured on the modified cell surface, wherein the target antibody captured on the modified cell surface is bound to an antigen, wherein the antigen is linked to a barcode nucleic acid molecule, and wherein the antibody secreting cell further comprises a nucleic acid molecule comprising the region of the gene encoding the antigen-binding fragment of the target antibody captured on the modified cell surface; b) hybridizing a portion of the barcode nucleic acid molecule to a portion of a first nucleic acid molecule attached to a solid surface; c) hybridizing a portion of the nucleic acid molecule comprising the region of the gene encoding the antigen-binding fragment of the target antibody captured on the modified cell surface to a portion of a second nucleic acid molecule attached to the solid surface; d) preparing a first library of amplicons of gene expression in the antibody secreting cell, a second library of amplicons of variable regions, diversity regions, and joining regions (VDJ) in the antibody secreting cell, and a third library of amplicons of antigen barcode nucleic acid molecules; e) sequencing each of the three libraries of amplicons; and f) identifying the region of the gene encoding the antigen-binding fragment of the target antibody captured on the modified cell surface.
In the above method, regarding step b) hybridizing a portion of the barcode nucleic acid molecule to a portion of a first nucleic acid molecule attached to a solid surface, in the partition (e.g., droplet), the partition (e.g., bead) dissolves and the cell barcode nucleic acid molecule/TSO oligos are free floating.
In the above method, regarding step c) hybridizing a portion of the nucleic acid molecule encoding the region of the gene encoding the antigen-binding fragment of the target antibody captured on the modified cell surface to a portion of a second nucleic acid molecule attached to the solid surface, the nucleic acid molecule comprising the region of the gene encoding the antigen-binding fragment of the target antibody captured on the modified cell surface (e.g., the BCR mRNA) does not directly hybridize. Rather, it is first made into first strand cDNA, and then the reverse transcriptase adds CCC to the end of the cDNA. The CCC then hybridizes to the rGrGrG part of the TSO. In addition, regarding the second nucleic acid molecule attached to the solid surface, in the partition (e.g., droplet), the partition (e.g., bead) dissolves and the second nucleic acid molecule is free floating.
In some embodiments, the modification of the modified cell surface comprises avidin, streptavidin, anti-biotin, biotin, the jun protein or a portion thereof, the fos protein or a portion thereof, the mad protein or a portion thereof, the max protein or a portion thereof, the myc protein or a portion thereof, an azide, an alkyne, and/or a phosphine. In some embodiments, the modification of the modified cell surface comprises avidin. In some embodiments, the modification of the modified cell surface comprises streptavidin. In some embodiments, the modification of the modified cell surface comprises biotin. In some embodiments, the modification of the modified cell surface comprises the jun protein or a portion thereof. In some embodiments, the modification of the modified cell surface comprises the fos protein or a portion thereof. In some embodiments, the modification of the modified cell surface comprises the mad protein or a portion thereof. In some embodiments, the modification of the modified cell surface comprises the max protein or a portion thereof. In some embodiments, the modification of the modified cell surface comprises the myc protein or a portion thereof. In some embodiments, the modification of the modified cell surface comprises an azide. In some embodiments, the modification of the modified cell surface comprises an alkyne. In some embodiments, the modification of the modified cell surface comprises a phosphine.
In some embodiments, the portion of the barcode nucleic acid molecule is complementary to a first template switch oligonucleotide (TSO). In some embodiments, the portion of the barcode nucleic acid molecule can be ligated to a first TSO. In some embodiments, a 3′ barcoded system can be used. In this case, the antigen barcode will have polyA. VDJ enrichment and sequencing may be performed differently.
In some embodiments, the portion of the first nucleic acid molecule attached to the solid surface comprises a first template switch oligo (TSO). In some embodiments, the 3′ terminus of the first nucleic acid molecule attached to the solid surface comprises a first sequence of three contiguous riboguanosine residues. In some embodiments, the first nucleic acid molecule attached to the solid surface further comprises a first unique molecular identifier (UMI). In some embodiments, the first nucleic acid molecule attached to the solid surface further comprises a first surface barcode. In some embodiments, the first nucleic acid molecule attached to the solid surface further comprises a first sequencing primer. In some embodiments, the first nucleic acid molecule attached to the solid surface comprises, from 3′ to 5′, the first sequence of three riboguanosine residues, the first TSO, the first UMI, the first surface barcode, and the first sequencing primer. In some embodiments, the first nucleic acid molecule attached to the solid surface is attached by the 5′ terminus of the first nucleic acid molecule attached to the solid surface.
In some embodiments, the first nucleic acid molecule attached to the solid surface comprises a first DNA molecule attached to the solid surface. In some embodiments, the first DNA molecule attached to the solid surface comprises a first single-stranded DNA molecule attached to the solid surface. In some embodiments, the portion of the first single-stranded DNA molecule attached to the solid surface comprises a first ISO and the first single-stranded DNA molecule attached to the solid surface beginning is reverse transcribed from the 3′ terminus of the portion of the barcode nucleic acid molecule which is complementary to the first TSO. Reverse transcription also occurs in the other strand as well, wherein the antigen barcode nucleic acid is extended from its 3′ and the first nucleic acid molecule attached to the solid surface is also extended from its 3′.
In some embodiments, the barcode nucleic acid molecule is a single-stranded DNA barcode nucleic acid molecule, wherein the portion of the first nucleic acid molecule attached to the solid surface comprises a first TSO, and the single-stranded DNA barcode nucleic acid molecule is reverse transcribed beginning from the 3′ terminus of the first TSO.
In some embodiments, the 3′ terminus of the portion of the barcode nucleic acid molecule comprises three contiguous cytidine or ribocytidine residues.
In some embodiments, an mRNA molecule encoding the region of the gene encoding the antigen-binding fragment of the target antibody captured on the modified cell surface is reverse transcribed, thereby generating a single-stranded DNA molecule encoding the region of the gene encoding the antigen-binding fragment of the target antibody captured on the modified cell surface. The actual chemistry occurs in solution in the partition (e.g., droplet).
In some embodiments, the nucleotide sequence of the single-stranded DNA molecule encoding the region of the gene encoding the antigen-binding fragment of the target antibody captured on the modified cell surface differs from a complement of the mRNA molecule encoding the region of the gene encoding the antigen-binding fragment of the target antibody captured on the modified cell surface in that the 3′ terminus of the single-stranded DNA molecule encoding the region of the gene encoding the antigen-binding fragment of the target antibody captured on the modified cell surface comprises three additional, contiguous cytidine or ribocytidine residues. In some embodiments, the 3′ terminus of the mRNA molecule encoding the region of the gene encoding the antigen-binding fragment of the target antibody captured on the modified cell surface comprises a plurality of contiguous adenine residues. In some embodiments, the 5′ terminus of the single-stranded DNA molecule encoding the region of the gene encoding the antigen-binding fragment of the target antibody captured on the modified cell surface comprises a plurality of contiguous thymine residues. In some embodiments, the 5′ terminus of the second nucleic acid molecule attached to the solid surface comprises a second sequence of three contiguous riboguanosine residues.
In some embodiments, the second nucleic acid molecule attached to the solid surface further comprises a second UMI. In some embodiments, the second nucleic acid molecule attached to the solid surface further comprises a second surface barcode. In some embodiments, the second surface barcode is the same surface (cell) barcode as the first nucleic acid molecule, in order to match antigen to BCR. In some embodiments, the second nucleic acid molecule attached to the solid surface further comprises a second sequencing primer. In some embodiments, the second nucleic acid molecule attached to the solid surface comprises, from 3′ to 5′, the second sequence of three riboguanosine residues, the second TSO, the second UMI, the second surface barcode, and the second sequencing primer. In some embodiments where a 10×genomics system is used, only the UMI is different for each of the nucleic acid molecules on the same surface. As long as the cell barcode is the same, the other components (e.g., ISO and sequencing primer) can be different. In some embodiments, the second nucleic acid molecule attached to the solid surface is attached by the 5′ terminus of the second nucleic acid molecule attached to the solid surface.
In some embodiments, the second nucleic acid molecule attached to the solid surface comprises a second DNA molecule attached to the solid surface. In some embodiments, the second DNA molecule attached to the solid surface comprises a second single-stranded DNA molecule attached to the solid surface. In some embodiments, the 3′ terminus of the portion of the second single-stranded DNA molecule attached to the solid surface comprises a second sequence of three contiguous riboguanosine residues. In some embodiments, the 3′ terminus of the portion of the nucleic acid molecule encoding the region of the gene encoding the antigen-binding fragment of the target antibody captured on the modified cell surface comprises three contiguous cytidine residues. In some embodiments, the second single-stranded DNA molecule attached to the solid surface is reverse transcribed beginning from the 3′ terminus of the three contiguous cytidine residues.
In some embodiments, the nucleic acid molecule encoding the region of the gene encoding the antigen-binding fragment of the target antibody captured on the modified cell surface comprises a second single-stranded DNA molecule encoding the region of the gene encoding the antigen-binding fragment of the antibody captured on the modified cell surface. In some embodiments, the 3′ terminus of the portion of the single-stranded DNA molecule encoding the region of the gene encoding the antigen-binding fragment of the target antibody captured on the modified cell surface comprises three contiguous cytidine or ribocytidine residues, and wherein the 5′ terminus of the portion of the second single-stranded DNA molecule attached to the solid surface comprises a second sequence of three contiguous riboguanosine residues. In some embodiments, the second single-stranded DNA molecule attached to the solid surface is reverse transcribed beginning from the 3′ terminus of the portion of the single-stranded DNA molecule encoding the region of the gene encoding the antigen-binding fragment of the target antibody captured on the modified cell surface. In some embodiments, the single-stranded DNA molecule encoding the region of the gene is reverse transcribed beginning from the 3′ terminus of the second single-stranded DNA molecule attached to the solid surface.
In some embodiments, the antibody secreting cell is disposed within a partition with the solid surface. In some embodiments, the partition contains a single antibody secreting cell. In some embodiments, the partition contains a single plasma cell or plasmablast. In some embodiments, the solid surface comprises a bead. In some embodiments, the antibody secreting cell within the partition is lysed. In some embodiments, the solid surface (e.g., bead) is dissolved upon partitioning and its surface-attached DNA molecules are released into solution within the partition. In some embodiments, the partition is an oil. In some embodiments, the partition is in the form of a droplet.
In some embodiments, the barcoded nucleic acid molecule further comprises a third sequencing primer.
In some embodiments, each amplicon is produced from a first library of amplicons that comprises the gene that encodes the antigen-binding fragment of the target antibody captured on the modified cell surface.
In some embodiments, the first library of amplicons is sample de-multiplexed, aligned, filtered, and UMI counted. In some embodiments, the sequencing of the first library of amplicons comprises next-generation sequencing.
In some embodiments, each amplicon of the first library of amplicons is mapped and aligned to a standard reference genome. In some embodiments, the standard reference genome comprises a human standard reference genome. In some embodiments, the human standard reference genome is GRCh38. In some embodiments, the standard reference genome comprises a murine standard reference genome. In some embodiments, the murine standard reference genome is mm10.
In some embodiments, each amplicon of the first library of amplicons is mapped to the standard reference genome with a single cell alignment software, such as STAR or kallisto (Bray et al., Nat. Biotechnol., 2016, 34, 525-527; Erratum in: Nat. Biotechnol., 2016, 34, 888), wherein each amplicon of the first library of amplicons comprises a unique molecular identifier, wherein all amplicons of the first library of amplicons which map to annotated genes of the standard reference genome are binned, and wherein the binned amplicons are counted for each unique molecular identifier (UMI), thereby generating a single cell count matrix comprising a mapped count for each annotated gene and a count for each UMI.
In some embodiments, the single cell count matrix is filtered for high quality cells and extensively profiled genes by calculating the ratio of the total number of annotated genes divided by the login of the total number of UMIs counted. In some embodiments, cells with a gene to UMI ratio below about 0.1 are filtered out. In some embodiments, cells with more than about four times the interquartile range of the total number of UMIs counted are filtered out. In some embodiments, cells with more than about 80% of reads map to a mitochondrial gene are filtered out. In some embodiments, cells with a gene to UMI ratio below about 0.1, cells with more than about four times the interquartile range of the total number of UMIs counted, and cells with more than about 80% of reads map to a mitochondrial gene are filtered out. In some embodiments, any threshold can be set for gene to UMI ratios and mitochondrial threshold. These values are highly dependent on the tissue being used. More stable tissues, such as blood and lymph nodes, require less stringent thresholds whereas tissue such as the gut, lung, or skin would have higher numbers of dead/dying cells with high mitochondrial contamination.
In some embodiments, the single cell count matrix is normalized such that the total number of UMIs counted is about 1,000, 5,000, 10,000, 20,000, 50,000, or 100,000. In some embodiments, the single cell count matrix is normalized such that the total number of UMIs counted is about 10,000. In some embodiments, the single cell count matrix is normalized such that the total number of UMIs counted is about 5,000. In some embodiments, the single cell count matrix is normalized such that the total number of UMIs counted is about 20,000.
In some embodiments, the principle component embeddings of the single cell count matrix are computed by principle component analysis (PCA) and are used as input to compute a uniform manifold approximation and projection (UMAP). Alternatively, tSNE projection could also be calculated from the PCA embeddings (van der Maaten et al., J. Mach. Learning Res., 2008, 9, 2579-2605). Additional iterative clustering of major cell types can be performed to identify similarities across batches. In some embodiments, the UMAP is generated using the methods disclosed in Korsunsky et al., Nat. Methods, 2019, 16, 1289-1296.
In some embodiments, cluster-specific centroids are used to determine a linear adjustment function per cell, applying the linear adjustment function per cell to correct for differences in batches, thereby generating batch corrected embeddings, and using the batch corrected embeddings to generate a uniform manifold approximation and projection (UMAP) in two dimensions. The method is called harmony (Korsunsky et al., Nat. Methods, 2019, 16, 1289-1296), however, several alternatives exist including the calculation of integration anchors from Seurat (Hao et al., Cell, 2021, 184, 3573-3587).
In some embodiments, a weighted k-neighbor graph is determined and the Leiden algorithm applied to the weighted k-neighbor graph with resolution values of about 0.1, about 0.2, about 0.5, and about 1.0 to determine cell type clusters in an unsupervised manner. In some embodiments, a weighted k-neighbor graph is determined and the Leiden algorithm applied to the weighted k-neighbor graph with resolution values of about 0.1 to determine cell type clusters in an unsupervised manner. In some embodiments, a weighted k-neighbor graph is determined and the Leiden algorithm applied to the weighted k-neighbor graph with resolution values of about 0.2 to determine cell type clusters in an unsupervised manner. In some embodiments, a weighted k-neighbor graph is determined and the Leiden algorithm applied to the weighted k-neighbor graph with resolution values of about 0.5 to determine cell type clusters in an unsupervised manner. In some embodiments, a weighted k-neighbor graph is determined and the Leiden algorithm applied to the weighted k-neighbor graph with resolution values of about 1.0 to determine cell type clusters in an unsupervised manner. Leiden is a community-detection algorithm that performs clustering iteratively by splitting nodes of similar cells to generate well-connected clusters (Traag et al., Scientific Reports, 2019, 9, 5233). Alternative algorithms include Louvain, K-means and NMF clustering.
In some embodiments, a pairwise Wilcox test is performed to all of the cells in one cluster and comparing the result of the first pairwise Wilcox test, and another pairwise Wilcox test is performed to all of the cells in every other cluster to quantify a p-value and fold-change for each gene in each cluster. In some embodiments, when a gene has a low p-value and the high fold-change, the cells are labeled by a common marker of antibody secreting cells and the cells are labeled by clustered subtypes that are named by the top genes from the differential expression result. This can be repeated for the cells with and without antigen specificity in each isotype (primarily IgE). In some embodiments, a test such as DESeq2 can be used for differential expression.
In some embodiments, sample de-multiplexing is performed, de novo assembly of read pairs into contigs accomplished, and the contigs against germline segment V(D)J reference sequences are aligned and annotated for the second family of amplicons.
In some embodiments, the alignment of the contigs against germline segment V(D)J reference sequences comprises aligning against a human germline reference database or a murine germline reference database using the software IgBlast (Ye et al., Nuc. Acids Res., 2013, 41, W34-W40). In some embodiments, the human germline reference database comprises the IMGT database of human germline immunoglobulin sequences (world wide web at “imgt.org/IMGTrepertoire/LocusGenes/”). In some embodiments, the murine germline reference database comprises the IMGT germline reference database.
In some embodiments, VDJ sequences are compared against sequences in the human germline reference database or the murine germline reference database, thereby labeling the VDJ sequences for quality alignments by checking for in-frame alignments, length of the CDR3, and/or the absence of stop codons in the variable region sequence and the VDJ sequences filtered based on the labels. In some embodiments, VDJ sequences are compared against sequences in the human germline reference database or the murine germline reference database, thereby labeling the VDJ sequences for quality alignments by checking for in-frame alignments. In some embodiments, VDJ sequences are compared against sequences in the human germline reference database or the murine germline reference database, thereby labeling the VDJ sequences for length of the CDR3. In some embodiments, VDJ sequences are compared against sequences in the human germline reference database or the murine germline reference database, thereby labeling the VDJ sequences for the absence of stop codons in the variable region sequence. Alternately, this step can be omitted to retain all possible VDJ sequences, which can be aligned to IgBlast to confirm high quality sequences that are in frame for human or mouse variable regions. This step may not be possible for less well-studied organisms if the database of germline VDJ sequences is not available.
In some embodiments, the VDJ sequences are mapped to a reference database (e.g., IMGT) of immunoglobulin chains.
In some embodiments, the immunoglobulin isotype, the variable region mapping, the joining region mapping, the diversity region mapping, the accuracy of full-length variable regions for both heavy and light chain sequence per cell are confirmed by the alignment. In some embodiments, the immunoglobulin isotype is confirmed by the alignment. In some embodiments, the variable region mapping is confirmed by the alignment. In some embodiments, the joining region mapping is confirmed by the alignment. In some embodiments, the diversity region mapping is confirmed by the alignment. In some embodiments, the accuracy of full-length variable regions for both heavy and light chain sequence per cell is confirmed by the alignment. In some embodiments, the VDJ sequences are mapped and annotated to the germline through IgBlast.
In some embodiments, the third library of amplicons is sample de-multiplexed, aligned, filtered, and UMI counted. In some embodiments, a single cell alignment software, such as STAR or kallisto, can be used.
In some embodiments, the third library of amplicons are mapped to a custom short-read reference which comprises the barcode nucleic acid molecule reference associated with each antigen. In some embodiments, the counts for each uniquely mapped barcode nucleic acid molecule are summed for each cell in a barcoded antigen single cell matrix.
In some embodiments, the barcode nucleic acid molecules across all cells are quantified and normalized by taking the centered log-ratio of each barcode nucleic acid molecule of the plurality of barcode nucleic acid molecules across each sample capture. Alternately, either centered log-ratio or denoising and scaling by background (DSB) can be used (Mule et al., bioRxiv, 2020.02.24.963603).
In some embodiments, the background antigen signal is removed by DSB for each barcode nucleic acid molecule of the plurality of barcoded nucleic acid molecules. Alternately, centered log-ratio can be used.
In some embodiments, an antigen signal distribution is determined, wherein when there is a well separated bimodal distribution in the antigen signal distribution, z-transformed values are used to compute antigen specificity, and wherein when there is not a well separated bimodal distribution in the antigen signal distribution, a quantile value is used. In some embodiments, rank order can be used rather than quantile value.
In some embodiments, the analysis of the first library of amplicons, the second library of amplicons, and the third library of amplicons is simultaneous to obtain at least one candidate sequence of the antigen-positive target antibody captured on the modified cell surface.
In some embodiments, antibody secreting cells with a valid antibody constant region are subset using the analysis of the first library of amplicons and the analysis of the second library of amplicons. In some embodiments, the antibody constant region comprises an IgE constant region. In some embodiments, the subsetted antibody secreting cell comprises detectable levels of IgE heavy chain and CD79a but lacking detectable levels of Ms4a1 and CD19, wherein the subsetted antibody secreting is an IgE plasma cell or plasmablast.
In some embodiments, the differential expression of the IgE antibody secreting cell is assessed against an IgA-secreting cell isotype, an IgG-secreting cell isotype, and/or an IgM-secreting cell isotype. In some embodiments, the assessment of differential expression further characterizes the unique transcriptional signature of the IgE antibody secreting cell.
In some embodiments, the antigen specificity of the IgE antibody secreting cell is assessed. In some embodiments, the assessment comprises comparing the antigen specificity of the IgE antibody secreting cell against a plurality of antigens and a control antigen, and wherein the plurality of antigens comprises the target antigen. In some embodiments, the comparing comprises calculating an empirical score for each antigen of the plurality of antigens and the control antigen by subtracting a quantile value of a signal associated with the antigen (qT) from a quantile value of a signal associated with the control antigen (qC) with a penalty factor (x) to determine an antigen specificity score where the antigen specificity score=qT−qCx. In some embodiments, the penalty factor is the same for all antigens. In some embodiments, the penalty factor is different for different antibody isotypes. In some embodiments, the penalty factor is different when other antigens are used.
In some embodiments, the antigen specificity score for each of the plurality of antigens and the control antigen is determined. In some embodiments, a control antigen specificity score is calculated, wherein when the antigen specificity score is high and the control antigen specificity score is low, selecting the cell. In some embodiments, the VDJ regions identify antigen-specific antibodies.
In some embodiments, antibody candidates are selected from a ranked list of antigen signals using the paired VH:VL antibody sequence of the cell.
In some embodiments, differential expression between isotypes, conditions, and/or antigen specificity is determined, wherein determining the differential expression between isotypes comprises performing a pairwise Wilcox test for all of the cells in one isotype and performing a pairwise Wilcox test for all of the cells in another isotype, thereby quantifying a p-value and fold-change of each gene for each cluster; and wherein determining the differential expression between antigen specificity comprises performing a pairwise Wilcox test for all of the cells in one isotype and performing a pairwise Wilcox test for all of the cells in another isotype, thereby quantifying a p-value and fold-change of each gene for each cluster.
There are many models/statistics for differential expression analysis. Some examples include: 1) “wilcox”, which identifies differentially expressed genes between two groups of cells using a Wilcoxon Rank Sum test (as described herein); 2) “bimod”, which is a likelihood-ratio test for single cell gene expression, (McDavid et al., Bioinformatics, 2013); 3) “roc”, which identifies “markers” of gene expression using ROC analysis; for each gene, evaluates (using AUC) a classifier built on that gene alone, to classify between two groups of cells; an AUC value of 1 means that expression values for this gene alone can perfectly classify the two groupings (i.e., each of the cells in cells. 1 exhibit a higher level than each of the cells in cells. 2); an AUC value of 0 also means there is perfect classification, but in the other direction; a value of 0.5 implies that the gene has no predictive power to classify the two groups; it returns a “predictive power” (abs(AUC-0.5)*2) ranked matrix of putative differentially expressed genes; 4) “t”, which identifies differentially expressed genes between two groups of cells using the Student's t-test; 5) “negbinom”, which identifies differentially expressed genes between two groups of cells using a negative binomial generalized linear model; 6) “poisson”, which identifies differentially expressed genes between two groups of cells using a poisson generalized linear model; 7) “LR”, which uses a logistic regression framework to determine differentially expressed genes; constructs a logistic regression model predicting group membership based on each feature individually and compares this to a null model with a likelihood ratio test; 8) “MAST”, which identifies differentially expressed genes between two groups of cells using a hurdle model tailored to scRNA-seq data; utilizes the MAST package in R to run the DE testing; 9) “DESeq2”, which identifies differentially expressed genes between two groups of cells based on a model using DESeq2 which uses a negative binomial distribution (Love et al., Genome Biol., 2014); and 10) “detection rate”, which identifies differentially expressed genes between two groups of cells based on percent detection rate between cell groups.
In some embodiments, VDJ sequence similarity in an antigen positive target cell are clustered, wherein the clustering VDJ sequence similarity comprises sequence-based alignment, grouping of similar variable regions by amino acid sequence.
In some embodiments, the antigen positive target cell is IgE+.
In some embodiments, redundant sequences are trimmed.
The present disclosure also provides methods of identifying a region of a gene encoding an antigen-binding fragment of a target antibody, wherein the target antibody is secreted by an antibody secreting cell, the method comprising: a) contacting a population of antibody secreting cells with a second component of a binding pair to allow the second component of the binding pair to bind to the cell surface, wherein the population of antibody secreting cells comprises the antibody secreting cell that secretes the target antibody; b) contacting the population of antibody secreting cells with an antibody capture complex, wherein the antibody capture complex comprises a first component of the binding pair linked to an antibody-capture molecule, whereby the first component of the binding pair binds to the second component of the binding pair on the cell surface of the population of antibody secreting cells, and whereby the antibody-capture molecule captures the target antibody secreted by the antibody secreting cell; c) contacting the population of antibody secreting cells with a secondary anti-Ig antibody, whereby the target antibody secreted by the antibody secreting cell and captured by the antibody capture complex binds the secondary anti-Ig antibody; d) contacting the population of antibody secreting cells with an antigen comprising a barcode nucleic acid molecule, whereby the target antibody secreted by the antibody secreting cell and captured by the antibody capture complex binds the antigen; e) collecting a pool of antibody secreting cells, wherein each cell in the pool secretes an antibody that is captured by the antibody capture complex, bound by the secondary anti-Ig antibody and by the antigen comprising the barcode nucleic acid molecule, and wherein the pool of antibody secreting cells comprises the antibody secreting cell that secretes the target antibody; f) separating the pool of antibody secreting cells into single antibody secreting cells, and for each single antibody secreting cell: 1) hybridizing a portion of the barcode nucleic acid molecule to a portion of a first nucleic acid molecule attached to a solid surface, wherein the solid surface and the first nucleic acid molecule attached thereto are unique to each single antibody secreting cell; 2) hybridizing a portion of the nucleic acid molecule comprising the region of the gene encoding the antigen-binding fragment of the target antibody to a portion of a second nucleic acid molecule attached to the solid surface; 3) preparing a first library of amplicons of gene expression, a second library of amplicons of variable regions, diversity regions, and joining regions (VDJ), and a third library of amplicons of antigen barcode nucleic acid molecules; and 4) sequencing each of the three libraries of amplicons; and g) identifying the region of the gene encoding the antigen-binding fragment of the target antibody.
In order that the subject matter disclosed herein may be more efficiently understood, examples are provided below. It should be understood that these examples are for illustrative purposes only and are not to be construed as limiting the claimed subject matter in any manner. Throughout these examples, molecular cloning reactions, and other standard recombinant DNA techniques, were carried out according to methods described in Maniatis et al., Molecular Cloning—A Laboratory Manual, 2nd ed., Cold Spring Harbor Press (1989), using commercially available reagents, except where otherwise noted.
Cells were washed and resuspended in PBS containing 5% w/v BSA. Surface Fc was blocked with 1:10 diluted Fc Block (eBioscience) along with detection of surface BCR (for cell line assays) for fifteen minutes at 4° C. The cells were washed twice more with PBS, spun down at 500 g for 10 minutes, resuspended in 1 mL of freshly prepared NHS-biotin (Sigma, 0.5 mg/mL in PBS) and incubated at 37° C. for fifteen minutes. The biotinylated cells were washed three times in cold PBS containing 5% w/v BSA with a changed tube for each washing step.
EctoFcεRIα was conjugated with streptavidin using a Lightning-Link® streptavidin conjugation kit to form the secreted IgE capture reagent. In brief, a solution of 0.5 mg/mL ectoFcεRIα containing 1 mg/mL streptavidin was prepared. One-hundred microliters of Modifier reagent was added to the solution with gentle mixing. The cap from the vial of Streptavidin Conjugation Mix was removed and the mixture, including the Modifier reagent, was added directly onto the lyophilized material. The material was resuspended gently by withdrawing and re-dispensing the added suspension once or twice using a pipette. The cap was replaced on the vial and the vial was stood for three hours in the dark at 20-25° C. Thereafter, 100 μL of Quencher reagent was added with gentle mixing. Thus, the secreted IgE capture reagent was generated.
Incubation of Cells Having Biotinylated Cell Surfaces with Secreted IgE Capture Reagent
Washed, biotinylated cells were resuspended at 1-3×106 cells/mL in 1 mL of PBS containing 5% w/v BSA and 30 μg/mL purified secreted IgE capture reagent and placed in six-well plates. In some embodiments, a volume up to 3 mL in six-well plates can be used. The cells were incubated at 37° C. for one hour on a rotating platform to allow for capture of secreted IgE. The cells were then washed twice in PBS containing 5% w/v BSA.
Tubes and reagents were prepared before lung samples were obtained. Ten milliliters of sterile water was added to 50 mg of Liberase® TH so as to have a final concentration of 26 collagenase Wunsch units/mL or 5.0 mg/mL collagenase. One milliliter aliquots were made into individual tubes and stored at −20° C. A Liberase® mix (digestion buffer) was prepared as needed:
For each mouse, 1.5 mL of the Liberase® mix was pipetted into a separate 5 mL flow cytometry tube. The tubes were kept on ice or in a cool rack until digestion was required.
For each mouse, the largest lobe of the right lung or the whole lung was placed in a separate 2 mL Eppendorf® tube with 1 mL of the Liberase® mix. In those tubes, the lung material was chopped into small pieces, typically cubes of about 2-3 mm. This material was incubated at 37° C. for twenty minutes. The digesting material was added to gentleMACS™ C Tubes and the digestion stopped by the addition of 0.5 M EDTA to a final concentration of 10 mM. Two milliliters of MACS® buffer was also added. The caps were screwed on tightly and the capped tubes were run on a gentleMACS™ Octo Dissociator using the preloaded program m_lung_02_01. The resulting cells were centrifuged at 400 g for four minutes and the supernatant was decanted. Red-blood cells in the pellet were lysed with 1 mL of Red-Blood Cell Lysing Buffer for three minutes at ambient temperature. Thereafter, 10 mL of DPBS was added to deactivate the lysing buffer. The cells were centrifuged at 400 g for four minutes, the supernatant decanted, and the pellet resuspended in 1 mL of DPBS. The suspension was filtered through a 100 μm Millipore® plate filter into a 2 mL deep-well plate. The cells were centrifuged at 400 g for four minutes and resuspended in 500 μL DPBS. Fifty microliters from each sample were pooled with 100 μL from other samples and the 150 μL pooled samples were added to round-bottomed 96-well plates.
To twelve-well, 70 μm cell strainer, plates 1-2 mL of RPMI media was added. The draining lymph nodes were collected and added to the plates. PCR plates were prepared and holes punched into each well with a 20 G needle and were placed on 2 mL deep-well plates.
The draining lymph nodes were mashed on a 74 μm cell strainer in 2 mL RPMI media using the back end of a 3 mL syringe. The preparation was filtered through a 100 μm Millipore® plate filter into a 2 mL deep-well plate and the filtered cells centrifuged at 400×g for four minutes. The pellet was resuspended in 500 μL DPBS and transferred to a 96-well deep-bottomed plate. This plate was centrifuged at 400×g for four minutes. The cells were resuspended in 200 μL of PBS. Into 96-well round-bottomed tubes were plated 200 μL of the suspension. The plate was centrifuged at 400×g for four minutes and the supernatant flicked off. The typical cell count from mice that had been administered intranasally 50 μg of HDM extract diluted in 20 μl of saline three times a week for fifteen weeks was 230×106 cells.
To 48-well plates, 200 μL of RPMI media was added. PCR plates were prepared and holes punched into each well with a 20 G needle and were placed on 2 mL deep-well plates.
The femurs of mice were extracted and the bones cleaned. Both ends of each bone were cut and placed in the PCR plate with holes. The PCR plate was placed on top of a 2 mL deep-well collection plate and centrifuged for four minutes at 500× g. The centrifugation step was repeated if any BM remained in the bones. The pellets were resuspended in 500 μL of red blood-cell lysis buffer was added. The suspension was incubated for three minutes at ambient temperature after which 1-2 mL of PBS was added to deactivate the lysis buffer. The resulting cells were centrifuged at 400×g for four minutes and the pellet resuspended in 1 mL DPBS. The suspension was filtered through a 100 μm Millipore plate filter into a 2 mL deep-well plate. From each sample, about 100-200 μL was taken for fluorescence minus one (FMO)s with the pool of the samples used for the FMO. Aliquoted, pooled samples were placed into twelve wells for the FMO. The remaining samples were centrifuged at 400×g for four minutes.
The bone-marrow samples were resuspended in 200 μL of PBS. Half of the bone-marrow sample was plated into 96-well round-bottomed plates. The plates were centrifuged at 400×g for four minutes and the supernatants flicked off. The typical cell count from mice that had been administered intranasally 50 μg of HDM extract diluted in 20 μl of saline three times a week for fifteen weeks was 116×106 cells.
Spleens were extracted from mice and homogenized in 5 mL DPBS in gentleMACS™ tubes using the pre-loaded program TBA. Homogenized spleens were centrifuged at 400×g for four minutes and supernatant was discarded. Spleens were then re-suspended in 4 mL red blood cell lysis buffer and incubated at room temperature for 5 minutes, after which 10 mL DPBS was added to neutralize the lysis buffer. Spleens were then centrifuged at 400×g for four minutes and the supernatant was discarded. Spleens were then re-suspended in 10 mL DPBS and filtered through 70 μM filters for single cell suspensions. Cell counts and viability were determined and the spleens were then stained for antigen+ B cells.
B cells were isolated using an EasySep® Mouse Pan-B cell Isolation Kit. In brief, the samples were prepared at 1×108 cells in 0.5-8 mL of PBS containing 5% w/v BSA. Fifty microliters of rat serum was added per mL of sample. The samples were added to 14 mL polystyrene round-bottom tubes (catalog no. 35205, lot no. 00421123). The cells were mixed and incubated for five minutes at ambient temperature. Fifty microliters of RapidSpheres® that had been vortexed for thirty seconds were added per milliliter of sample and the mixture was incubated at 2.5 minutes. Phosphate-buffered saline containing 5% w/v BSA was added to a volume of 5 mL and the tubes placed inside The Big Easy EasySep® magnet (StemCell catalog no. 18001) for 2.5 minutes at ambient temperature. The enriched cell suspension was poured into a new tube and counted. An overview of the procedure is set forth below:
To pair secreted antibodies to the ASCs secreting them, immunoglobulin capture complexes were derived that can locally capture secreted antibodies on the surface of ASCs (
To determine functionality, sensitivity and specificity of IgG and IgE capture complexes, ARH77, an IgG (kappa light chain) secreting cell line, and U266, an IgE (lambda light chain) secreting myeloma line were used for proof of principle experiments (
To test specificity of the capture complex, IgM-expressing Ramos cells were mixed with U266 cells 1:1 (
An approach was made to pair a given secreted IgE antibody with the PC that secreted the antibody.
The surfaces of IgE-secreting U266 cells were biotinylated as described herein, washed three times in cold PBS with 5% w/v BSA with the tubes changed for every wash step, and incubated with the secreted IgE capture reagent as described herein. Thereafter, the cells were washed and stained for thirty minutes at 4° C. with Brilliant™ Violet 711-labeled anti-IgE (BD) in PBS with 5% w/v BSA, 10 mg/mL dextran sulfate, and 1:50 Fc block. The cells were then washed with 10× Brilliant™ Violet buffer. Thereafter, the cells were washed twice in PBS and fixed with BD Cytofix™. Subsequently, flow cytometric data was acquired.
The secreted IgE capture reagent was found to specifically capture secreted IgE antibody on the surface of U266 cells (
IgEVenus and Blimp-1mCherry reporter mice were used to determine if the secreted IgE capture reagent could capture secreted IgE on the surface of IgE-producing, primary plasma cells. Specifically, the Venus reporter, which had been inserted downstream of membrane IgE locus, identified IgE-secreting cells while the mCherry reporter, which had been inserted downstream of Blimp-1, identified PCs (Asrat et al., Sci. Immunol., 2020, 10, eaav8402). The mice were challenged with 50 μg of HDM extract diluted in 20 μl of saline solution administered intranasally three times a week for fifteen weeks. The mice were anesthetized and sacrificed as described herein. The BM cells were prepared as described herein and the LDLNs were prepared as described herein. BM from mice were pooled together and, separately, dLN from mice were pooled together. Pan-B cells were isolated and stained with an antibody mix comprising Brilliant™ Violet 711 labeled anti-IgE (BD) to detect secreted IgE in PBS with 5% w/v BSA for thirty minutes at 4° C. The labeled cells were washed in PBS with 5% w/v BSA, fixed with Cytofix™, and sorted with a BD FACSymphony® S6 flow cytometer (
Plasma cells were prepared as described in Example 3. Single PCs were suspended in PBS with 0.04% w/v BSA and loaded onto a Chromium® Controller device (10× Genomics) at 15,000 cells per lane. Partitions of the PCs in barcoded beads were formed and the PCs lysed. Reverse transcription was performed followed by breakdown of the partition. RNA-seq, Feature Barcode, and V(D)J libraries were prepared using a Chromium® Next GEM Single Cell 5′ Kit, v.2 (10× Genomics). After amplification of the libraries, cDNA was split into separate RNA-seq, Feature Barcode, and V(D)J aliquots. To enrich the V(D)J aliquot for BCR sequences, the Chromium® Automated Single Cell Mouse and Human BCR Amplification & Library Construction Kit (10× Genomics) was used. Feature Barcode libraries for DNA-barcoded Antigens or DNA-barcoded cell surface proteins were prepared using a Chromium® 5′ Feature Barcode Library Construction kit (10× Genomics). Paired-end sequencing was performed on an Illumina NovaSeq® 6000 sequencing system for RNA-seq libraries with read 1 being 26 bp for unique molecular identifiers (UMIs) and cell barcodes and read 2 being 80 bp for transcript reads, with 10 bp i7 and 10 bp i5 reads. Pair-end sequencing was also performed feature barcode libraries with read 1 being 26 bp for UMIs and cell barcodes, read 2 being 35 bp for feature barcode read, and with 10 bp i7 and 10 bp i5 reads. Pair-end sequencing was also performed for V(D)J libraries with read 1 being 150 bp, 10 bp for i7, 10 bp for i5, and Read 2 being 150 bp. For RNA-seq and Feature Barcode libraries, the Cell Ranger Single-Cell Software Suite, version 6.1.1 (10× Genomics) was used to perform sample de-multiplexing, alignment, filtering, and UMI counting. The human GRCh38 and mouse mm10 genome assembly and RefSeq gene model for humans and mice, respectively, were used for alignment. For V(D)J libraries, the Cell Ranger software was used to perform sample de-multiplexing, to de novo assemble of read pairs into contigs, to align, and to annotate contigs against all V(D)J germline reference sequences from the germline mouse IMGT reference database.
The single cell gene expression library was mapped and aligned to the standard mouse reference genome Mm10. Subsequently, the unique mapped counts for each gene were determined by the CellRanger software. Reads were mapped to the standard reference genome with a single cell alignment software STAR, where each read comprises a unique molecular identifier which maps to annotated genes of the standard Mm10 reference genome. The mapped reads were binned and counted for each unique molecular identifier (UMI), thereby generating a single cell count matrix comprising of mapped counts for each annotated gene and a count for each UMI. The single cell-count matrix was then filtered for by calculating the ratio of the total number of annotated genes divided by the login of the total number of UMIs counted. Cells with a gene to UMI ratio below about 0.1 were filtered out. Cells with more than four times the interquartile range of the total number of UMIs were filtered out. Cells with more than about 80% of reads map to a mitochondrial gene were filtered out. High quality cells with a gene to UMI ratio above about 0.1, with less than about four times the interquartile range of the total number of UMIs counted, and with less than 80% of reads mapping to a mitochondrial gene were retained. The count matrices from each individual sample capture were normalized to a total count of 10,000 and batch corrected using the Harmony algorithm to generate a combined uniform manifold approximation and projection (UMAP). Unsupervised clustering by the Leiden algorithm was then used to determine cell type clusters and a Wilcox test was used to identify specific cell type and cluster marker genes.
The IgBlast sequence analysis tool (Ye et al., Nucleic Acids Res., 2013, 41, W34-W40) was carried out to align the V(D)J sequences against the germline mouse IMGT reference database. Valid V(D)J sequences were then filtered by productive in-frame alignments, full-length CDR3s, and the absence of stop codons within the sequence. The IgBlast tool also confirmed the immunoglobulin isotype, gene mappings for variable, diverse, and joining regions, and accurate full-length variable regions for both heavy and light chain sequences per cell.
The barcoded antigen library was mapped by the CellRanger software to a custom short-read reference that contained the DNA tag sequences of the four barcoded antigens, namely, Der p 1, Der p 2, Der f 1 and Ole e 1. These tag sequences were quantified across all cells and were normalized by taking the centered log-ratio (CLR) per barcoded antigen across each sample capture. In addition, background antigen signal for each barcoded antigen was removed by DSB (Denoised and Scaled by Background). Both the CLR and the DSB normalized values were used to quantify the target antigen signals, namely, those for Der p 1, Der p 2 and Der f 1, against the control signal, namely, that for Ole e 1.
Antigen specificity score (AgSS) for IgG were calculated by subtracting the quantile of hIL-6Rα barcoded UMI counts multiplied by a penalty factor (x) from the quantile of hIL-4Rα barcoded UMI counts, AgSS=QhIL-4Rα-QhIL-6Rαx. AgSS for IgE were calculated with a similar formula for mouse and human single cell data. For IgE scores the target antigens were either Der p1, Der p2 or Der f1 and the control was always Ole e1.
Ig BCR sequences were clustered using scirpy v0.10 using the function scirpy.pp.ir_dist based on the amino acid sequence and with a hamming distance of less than 4. Clustered BCRs were collected into clonotypes with the function scirpy.tl.define_clonotypes based on the heavy chain CDR3 amino acid sequence based on the previous criteria of a hamming distance of less than 4. Scirpy documentation can be referenced at the world wide web at “scverse.org/scirpy/latest/api.html”.
Following processing of the three single-cell libraries, the gene expression and V(D)J region sequencing data were used to subset PCs with a valid IgE constant region and detectable expression of IgE and CD79a but lacking the expression of Ms4a1 and CD19 typically found in non-PC B cells. IgE-expressing PCs were then assessed for differential expression against additional IgA, IgG, and IgM plasma cell isotypes to further characterize the unique transcriptional signature of IgE-secreting PCs. IgE-secreting PCs were then assessed for antigen specificity by comparing the normalized levels of the target antigens, namely, Der p 1, Der p 2, or Der f 1, against the normalized level of the control antigen Ole e 1. This was performed by calculating an empirical score for each target antigen and subtracting the quantile rank of the target antigen from the quantile rank of the control antigen with a penalty factor. The formula used to do is set forth below:
Antigen specificity=qT−qCx
where qT refers to the quantile of the target signal, qC refers to the quantile of the control signal, and x is a penalty factor.
The antigen specificity score (AgSS) was determined per cell for each of the three target antigens and utilized to prioritize cells with the strongest signal of target antigen while minimizing the signal of the control antigen. Antibody candidates were selected from the ranked lists of target antigen signal using paired VH:VL antibody sequences from the cell in question.
After selecting allergen-specific antibodies, relative binding to Der p 1, Der p 2, and Der f 1 were quantified by ELISA.
For validation of IgE capture in vivo, the previously described IgEVenus and Blimp-1mCherry reporter mice (
To elucidate the biology of tissue resident IgE PCs, the single-cell transcriptomic profiles from lung dLN and BM were merged and cell clustering to compare IgE, and non-IgE PCs was performed. 12,646 IgG+ cells, 17,524 IgA+ cells, 3,503 IgM+ cells and 1,703 IgE+ cells were obtained (
Using-barcoded HDM allergens, it was possible to directly map IgE PCs to their specificity to Der p1, Der p2, Der f1 (HDM allergens) and Ole e1 (olive allergen, negative control) and compare their AgSS which were calculated as described in Example 4. The antigens were Der p1, Der p2 and Der f1, and the control for all was Ole e1 (olive antigen) (
A few allergen-specific IgE antibodies were selected based on reactivity profile (see, Table 3) and their relative binding to Der p1, Der p2 and Der f1 as well as to the olive allergen, Ole e1, was tested by ELISA. 2 IgE antibodies (IgE mAb12_2 and mAb 3_1) bound to Der p1 (
To determine if the IgEs that showed HDM-allergen binding had anaphylactic potential, a passive cutaneous anaphylaxis (PCA) assay was performed. Mice were sensitized intradermally with a cocktail of Der p1 or Der p2 specific IgEs (
To determine if IgE secretion capture could be extended to human primary cells, we performed IgE-secretion capture on the BM of self-reported allergic donors. B lineage enriched cells were coated with NHS-biotin and secreted IgE was captured using StAv-FcεRIα ectodomain as previously described in
Following sorting, scRNA-seq recovered full transcriptomes and BCR sequences of 5,559 bone marrow PCs from the cat, grass, and dust allergic individual. The specificity of PC capture was confirmed based on the abundant expression of various immunoglobulin genes and PC markers such as XBP1, SLAMF7, and CD74, but B cell markers such as MS4A1 and CD19 were not observed (
To investigate clonal evolution, VH sequences from all 5,559 cells were clustered based on the amino acid sequence of the heavy chain CDR3 region allowing for up to 3 amino acid mismatches, deletions, or insertions. The 10 IgE PCs clustered uniquely into 5 clonotypes, which were defined as a group of PCs with highly similar heavy chain amino acid CDR3s (see, Table 4). Two clonotypes, denoted 753 (n=4 cells) and 696 (n=3 cells), were made up exclusively of IgE cells and each clonotype displayed identical CDR3 sequences, respectively (
After selecting the IgE clones, we tested binding of the purified IgEs and a control (DNP-IgE) to relevant allergens to which the donor was allergic to (Fel d1 for cats, Der p1 for dust or Can e1 for dog as a control) by ELISA (
An anti-mouse IgK antibody was conjugated with streptavidin using a Lightning-Link® streptavidin conjugation kit to form the secreted IgG capture reagent. In brief, a solution of anti-mouse IgK antibody containing 1 mg/mL streptavidin was prepared. One-hundred microliters of Modifier reagent was added to the solution with gentle mixing. The cap from the vial of Streptavidin Conjugation Mix was removed and the mixture, including the Modifier reagent, was added directly onto the lyophilized material. The material was resuspended gently by withdrawing and re-dispensing the added suspension once or twice using a pipette. The cap was replaced on the vial and the vial stood for three hours in the dark at 20-25° C. Thereafter, 100 μL of Quencher reagent was added with gentle mixing. Thus, the secreted IgK capture reagent was generated.
To detect antigen-specific IgG-secreting PCs, the footpads of VI3/VelocImmune mice were immunized twice a week for four weeks with an immunogen. The mice were rested for a month then boosted with immunogen four days before anesthesia, sacrifice, and procurement of the BM, Spleen, and Draining Lymph Nodes. Cells from the bone marrow, spleen, and draining-lymph nodes were prepared as described herein. Single-cell preparations from the spleen and lymph nodes were pooled and surface Fc receptors blocked with 1:10 diluted Fc Block for fifteen minutes at 4′C. The pooled preparations were then stained using an antibody cocktail to gate for antigen-specific IgG B cells (
For IgG-secreting PCs for which the IgG had been captured, libraries for gene expression, the V(D)J regions of the secreted IgG, and barcoded antigens were prepared and sequenced in the manner described in Example 3. The individual libraries were also mapped, quantified, normalized, and processed in the manner described in Example 4. Owing to the humanized nature of the V(D)J region of the VelocImmune® mice, the V(D)J library was mapped to the standard human germline IMGT reference. Following processing of the three single-cell libraries, the gene expression and V(D)J region sequencing data were used to subset PCs with a valid IgG constant region and detectable expression of IgG and CD79a but lacking the expression of Ms4a1 and CD19 typically found in non-PC B cells. In order to select antigen-specific, IgG-expressing PCs, the antigen specificity score was calculated for the target immunogen against a control antigen (hIL-6Rα) as described in Example 4. Results are shown in
To test antigen-specificity and IgG expression of BCR sequences from the IgG secretion trap, hIL-4Rα antigen or anti-human IgG (Jackson Labs) was plated at 1 ug/mL or 2 ug/mL, respectively, overnight at +4° C. The next day, plates were washed three times in PBS supplemented with 0.05% Tween20 (PBS-T) and blocked with PBS with 0.5% BSA for 1 hour at room temperature. Plates were subsequently washed three times with PBS-T, and diluted supernatants from Expi293F cells transfected with individual BCRs from the BMPC, PB/PC-like, or Spleen B-cell fractions were plated for 1 hour at room temperature. Plates were then washed three times with PBS-T and incubated with an anti-human IgG-HRP antibody (Jackson Labs) at 1:10,000 for 1 hour at room temperature. Plates were washed three times in PBS-T, developed using TMB substrate, stopped using 1N sulfuric acid, and read at 450 nm.
As described in
As shown in
scRNA-seq was performed on sorted BMPCs, splenic/dLN B cells, and PBs/PCs to determine transcriptional differences, identify VH:VL repertoire changes and quantify antigen specificity at a single cell level. From barcoded antigen counts of hIL-4Rα and a negative control antigen hIL-6Rα, Ag+/IgG+ cells were verified (
scRNA-seq yielded three distinct cell populations: bone marrow plasma cells (BMPCs), spleen/dLN plasmablast/plasma cell-like (Sp/dLN PBs/PCs), and spleen/dLN B cells (Sp/dLN B cells). From each of these populations, 20 unique VH:VL sequences from cells with the highest hIL-4Rα barcode signal were selected for cloning and expression analysis (
Consistent IgG expression was observed across all three populations, but anti-hIL-4Rα activity was observed in 80% (16/20) of BMPCs compared to 32% (6/19) and 53% (10/19) of Sp/dLN PBs/PCs and Sp/dLN B cells, respectively (
Following validation of Ag+ cells, we investigated the unique BCR sequences obtained by scRNA-seq of the VDJ region to compare Ag+ BMPCs with B and PBs/PCs from the spleen/dLN. BCR sequences from all cells were mapped to specific V, D and J gene segments by IgBlast and the extent of somatic hypermutation was measured by percent similarity to germline V regions. Ag+ cells in all three compartments exhibited lower percent similarity to germline V regions and therefore more frequent mutations than non-Ag+ cells (
In addition to BCR sequence analysis, the transcriptomes of Ag+ and non-Ag+ cells in each of the three compartments were also compared to identify gene signatures related to hIL-4Rα specificity. In BMPCs, several gene expression programs differed based on hIL-4Ra specificity (
In this Example, TRAPnSeq was used to isolate vaccine-specific IgG+ plasma cells (PCs) from human bone marrow. After enrichment for B cells and antibody secreting cells (ABCs), cells were biotinylated with NHS-biotin, and an affinity matrix was assembled using streptavidin coupled to anti-human Igk (StAv-algk) to capture secreted IgG. Following assembly of biotin—StAv-algk complex on the surface, enriched B cells/ASCs were stained with an antibody mix containing PC-specific markers, αlgG for detection of secreted IgG, and fluorescent-tagged antigens (listed in the table below) for detection of Ag+ cells.
After gating on PCs as CD20-CD38++(
The workflow of a secretion trap combined with antigen chase is illustrated in
Biotinylated human IL-4 Receptor a (hIL-4Rα) ectodomain was conjugated to PE-labeled streptavidin (“SA-PE”) tetramer overnight at 4′C. Separately, a trap antibody (mouse anti-human IgG (BD cat #555784, Clone #G18-145)) was conjugated to streptavidin overnight using a commercially available kit (abcam cat #ab102921).
A25 cells were suspended in NHS-biotin (Sigma cat #203112) at final concentration of 0.5 mg/mL in DPBS/FBS for 15 min at 37° C. A25 cells were derived from the commercially available A20 line by knocking out the endogenous surface BCR. Thus, A25 cells are mouse B cells without surface or secreted BCR.
After incubation, the cells were washed 3 times in DPBS/FBS, with transfer to a new conical tube after each wash to remove residual biotin.
Biotinylated cells were incubated with or without streptavidin conjugated trap antibody (or “SA-anti-hulgG”), performed at 1:100 dilution) at 10 million cells/mL in DPBS/FBS for about 15 minutes at 4° C. The 1:100 cell versus trap antibody ratio ensured that the trap reagent was bound to all biotinylated cells prior to spiking in the antibodies in the next step. After incubation, the cells were washed twice in DPBS/FBS and then resuspended in DPBS/FBS.
The following four antibodies differing in affinity were used. Each individual antibody was spiked into a cell suspension at about 1 mg antibody per 2 million cells. After incubation, the cells were washed twice in DPBS/FBS.
Next, the cells were incubated with 5 nM hIL-4Rα labeled with AlexaFluor 647 (“AF647”) for 30 min at room temperature (RT) in DPBS/FBS. After incubation, the cells were washed twice in DPBS/FBS.
Afterwards, the cells were incubated with pre-conjugated hIL-4Rα biotin-StAv-PE twice for 45 min (or 2×45 min) at RT in DPBS/FBS. The concentration for antigen hIL-4Rα was nM. After incubation, the cells were washed twice in DPBS/FBS, and analyzed by flow cytometry. As shown in
As a control, after the chase antigen incubations (hIL-4Rα-biotin-StAv-PE), cells were washed twice in DPBS/FBS and then stained with an anti-hulgK-PE-Cy7 antibody to detect antibody on the surface of the cells. Ab 4/neg control did not stain for antigen, but it was positive for IgK, indicating that the antibody was still captured on the surface of the cells.
The disclosure provides the following illustrative embodiments:
Various modifications of the described subject matter, in addition to those described herein, will be apparent to those skilled in the art from the foregoing description. Such modifications are also intended to fall within the scope of the appended claims.
| Number | Date | Country | |
|---|---|---|---|
| 63319883 | Mar 2022 | US | |
| 63433728 | Dec 2022 | US |
