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  • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
  • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
  • C12N15/09—Recombinant DNA-technology
  • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
  • C12N15/1034—Isolating an individual clone by screening libraries
  • C12N15/1065—Preparation or screening of tagged libraries, e.g. tagged microorganisms by STM-mutagenesis, tagged polynucleotides, gene tags
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
  • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
  • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
  • C07K16/2896—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against molecules with a "CD"-designation, not provided for elsewhere
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
  • C07K16/40—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against enzymes
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
  • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
  • C12Q1/02—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving viable microorganisms
  • C12Q1/025—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving viable microorganisms for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
  • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
  • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • C12Q1/6869—Methods for sequencing
• • C—CHEMISTRY; METALLURGY
  • C40—COMBINATORIAL TECHNOLOGY
  • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
  • C40B20/00—Methods specially adapted for identifying library members
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
  • C07K2317/56—Immunoglobulins specific features characterized by immunoglobulin fragments variable (Fv) region, i.e. VH and/or VL
• • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
  • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
  • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
  • Y02A90/00—Technologies having an indirect contribution to adaptation to climate change
  • Y02A90/10—Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation

Definitions

• This invention generally relates to a method of isolating from a large number of cells, a cell producing an antibody of interest. More particularly, the invention relates to indentifying antibodies of interest being produced by a cell and determining the sequence which encodes the antibody.
• the first is protein complex formation via covalent bonds such as the heavy chain and light chain of an immunoglobulin.
• the second is protein-protein association via non-covalent bonds exemplified by heterodimer formation of HER-2 and EGFR (epidermal growth factor receptor).
• the third is an association between 2 molecules involved in a cellular pathway such as a cytokine receptor and a caspase in an apoptosis pathway.
• Antigen binding proteins involved in the immune response are present in mammals as large polyclonal repertoires representing a broad diversity of binding specificities. This diversity is generated by rearrangement of gene sequences encoding variable regions of these binding proteins.
• variable region binding proteins include soluble and membrane-bound forms of the B cell receptor (also known as immunoglobulins or antibodies) and the membrane-bound T cell receptors (TCR).
• B cell receptor also known as immunoglobulins or antibodies
• TCR membrane-bound T cell receptors
• affinity maturation which involves cycles of somatic hypermutation of these variable genes.
• Heterohybridomas i.e., fusion of human B cells with mouse myeloma cells, were attempted but they are extremely unstable and thus rarely lead to suitable cell lines for production purposes.
• variable region encoding sequences for example heavy chain variable region and light chain variable region encoding sequences
• the variable region encoding sequences which are to constitute the library can be amplified from lymphocytes, plasma cells, hybridomas or any other immunoglobulin expressing population of cells.
• Current technologies for generating combinatorial libraries involve separate isolation of the variable region encoding sequences. Thus, the original pairing of, for example, immunoglobulin heavy chain variable region and light chain variable region encoding sequences is lost. Said sequences are randomly paired and the original combinations of these variable sequences only occur by chance.
• variable region encoding sequences responsible for a desired binding specificity a considerable amount of screening is necessary. This is typically performed in combination with methods for enrichment of clones exhibiting a desired specificity, such as ribosome display or phage display. Even then, the diversity achieved might not be sufficiently large to isolate variable region encoding sequence pairs giving rise to binding proteins of similar high affinity as those found in the original cells. Further, the enrichment procedures normally used to screen combinatorial libraries introduce a strong bias, e.g. polypeptides of particular low toxicity in E. coli, efficient folding, slow off-rates, or other system dependent parameters, thus reducing the diversity of the library even further.
• cognate pairs In addition, clones derived from such combinatorial libraries will be more prone to producing binding proteins with cross reactivity against self-antigens because they, in contrast to original pairs (hereafter called cognate pairs), have never been subjected to in vivo negative selection against self-antigens as pairs, such as is the case for B- and T-lymphocyte receptors during particular stages of their development. Therefore, the identification of cognate pairs of variable region encoding sequences is a desirable approach.
• the frequency of clones exhibiting a desired binding specificity is expected to be considerably higher within a library of cognate pairs than in a conventional combinatorial library, particularly if the starting cells are derived from a donor with high frequency of cells encoding specific binding pairs, e.g., immune or immunized donors.
• variable region encoding sequences derived from the same cell In order to generate cognate pair libraries the linkage of the variable region encoding sequences derived from the same cell is required. At present, 3 different approaches that achieve cognate pairing of variable region encoding sequences have been described.
• In-cell PCR is an approach where a population of cells is fixed and permeabilized, followed by in-cell linkage of heavy chain variable region and light chain variable region encoding sequences from immunoglobulins. This linkage can be performed either by overlap extension RT-PCR or by recombination.
• the amplification process is a three to four step process consisting of i) reverse transcription utilizing constant region primers generating immunoglobulin cDNA, ii) PCR amplification of the heavy and light chain variable region encoding sequences utilizing primer sets containing either overlap- extension design or recombination sites, iii) optional linkage by recombination, and iv) nested PCR of the products generating restriction sites for cloning. Since the cells are permeabilized there is a considerable risk that amplification products might leak out of the cells, thereby introducing scrambling of the heavy chain variable region and light chain variable region encoding sequences, resulting in the loss of cognate pairing. Therefore, the procedure includes washing steps after each reaction which makes the process laborious and reduces the efficiency of the reactions.
• the in-cell PCR is extremely inefficient, resulting in low sensitivity. Accordingly, the in-cell PCR linkage technique has never found widespread usage, and the original studies have never been reliably repeated in a way that can verify that the linkage actually occurs within the cell. This, however, is absolutely crucial to avoid scrambling the heavy chain variable region and light chain variable region encoding sequences and thereby disrupting the cognate pairs.
• Single-cell PCR is a different approach to achieve cognate pairing of heavy chain variable region and light chain variable region encoding .
• a population of immunoglobulin expressing cells are distributed by diluting to a density of one cell per reaction, thereby eliminating scrambling of heavy chain variable region and light chain variable region encoding sequences during the cloning process.
• the process described is a three to four step procedure consisting of i) reverse transcription utilizing oligo-dT-, random hexamer- or constant region primers generating cDNA, ii) fractionating the cDNA product into several tubes and performing PCR amplification on the individual variable chain encoding sequences (in separate tubes) with primer sets containing restriction sites for cloning, iii) nested PCR of the products generating restriction sites for cloning (optional) and iv) linking the heavy chain variable region and light chain variable region encoding sequences from the separate tubes by cloning them into an appropriate vector, which is itself a multi-step process.
• Symphogen's (Symphogen A/S, Lyngby, Denmark) approach is to use multiplex overlap-extension RT-PCR (reverse transcription-polymerase chain reaction) to identify the natural pairing of heavy chain and light chain antibodies by isolating single B cells in a well of a 96- well microtiter plate.
• RT-PCR reverse transcription-polymerase chain reaction
• PCR primer based DNA barcoding has been described in the literature. There have been studies utilizing oligonucleotide tags to label DNA molecules during sample preparation such that after sequencing by a massively parallel technology, one is able to digitally sort DNA sequences originating from different samples or a positive control. However, each tagging PCR primer must be individually synthesized. As such, when a large number of samples are processed, this practice will become prohibitively expensive. Consequently, the technique is only suitable for a limited number of samples.
• the invention is a methodology which makes it possible to select from a very large number of cells, a single cell or cells of interest and obtain specific information from those cells in a rapid and efficient manner.
• a large number of antibody producing cells such as plasma cells are separated so that these individual antibody producing plasma cells are placed in individual wells.
• the cells are allowed to produce antibodies and the antibodies in the wells are then contacted with a protein bound to a solid surface such as a well top.
• the protein universally and specifically binds antibodies in the wells.
• the surface or well tray top includes addresses configured such that each address is specifically related to one of the individual wells containing a cell producing antibodies.
• Information relating to the antibodies which bind the protein on the surface is then obtained.
• the information can be the binding affinity of the antibodies at a particular address for a particular known antigen.
• the information at all of the addresses may be analyzed or screened simultaneously in order to find the address or particular group of addresses which are of particular interest such as antibodies with a high binding affinity to the particular known antigen.
• the screening of the antibodies can be done by contacting the antibodies with antigens of interest which antigens may be labeled. After identifying the addresses of the antibodies of interest those addresses are correlated to the well or wells of interest.
• Information relating to the DNA sequence of the antibodies is then obtained and correlated with said antibodies of interest. This is done by lysing the antibody and then isolating mRNA encoding the antibodies of interest.
• the cDNA may be sequenced and the cDNA may be used to genetically engineer cells which produce antibodies of interest.
• the cDNA may be synthesized to incorporate specific tags that correlate to the physical location of wells, the physical location of antibodies on the surface, and the DNA sequence.
• the specific tags allow the pooling of cDNA from all wells for subsequent determination of the individual cDNA sequences.
• the sequences of particular interest are those encoding the light and heavy chain variable regions or portions thereof sufficiently large to construct an antibody of interest.
• the sequences of the light and heavy chain of each antibody are associated using the specific tags.
• the methodology can be used with hundreds, thousands, tens of thousands, hundreds of thousands, millions or more cells at the same time. By using this technique it is possible to sort through large numbers of cells quickly and identify those cells which produce antibodies of interest and relate those antibodies directly to the nucleotide sequence responsible for producing the antibodies desired.
• the present invention provides an efficient method for analyzing a large number of cells.
• the present invention solves the problem of reporting the average measurement for a population of cells.
• cells are separated and processed in small microwells where diffusion of molecules among micro wells is retarded or blocked.
• each microwell due to its small dimensions, facilitates rapid reaction rates, such as mRNA hybridization or capture of proteins.
• mRNAs from target genes are captured by oligonucleotide probes located inside each microwell. Simultaneously, corresponding protein(s) or protein complexes are retained by a capture agent confined to each microwell.
• Conversion of the captured mRNA into double-stranded cDNA incorporates an oligonucleotide tag unique to each microwell.
• the cDNA can then be pooled and sequenced by ultra-high throughput DNA sequencing technology to determine the structure of each member of the protein complex in each originating cell.
• the captured proteins form an array on a substrate where their kinetic properties can be analyzed when contacting with labeled affinity ligands common to all captured proteins or complexes. Such measured kinetic properties can be used to a) rank the protein complexes with respect to affinity b) filter DNA sequence data thereby removing contaminating or irrelevant cells from consideration, c) classify the type of cell based on the quantity of protein complex, or d) measure the frequency of cells producing similar protein complexes.
• the frequency at which cells produce a particular protein such as an antibody it is possible to determine various characteristics regarding antibodies which might be produced in response to a particular antigen and also determine additional information which may be useful in characterizing desirable antibodies.
• the protein complex under study can be the heavy chain and light chain of an antibody.
• integrating structural information with kinetic properties provides insights into the paratopes on the antibody as well as the epitopes on the antigen.
• simulation with antibodies against the hapten 2-phenyl-5-oxazoIone (phOX) was performed.
• the present invention has many potential uses but a major application is likely to be the analysis of gene combinations that are polymorphic within a population of cells, such as the rearranged genes for Ig or T cell receptors or secreted antobodies.
• the present invention provides a method for characterizing molecular interactions within a single cell. This is accomplished by determining the structure of cis- and/or trans-protein complexes and optionally measuring binding kinetic properties between said cis- and/or trans-protein complexes and a ligand.
• the invention separates a plurality of cells into a plurality of microwells wherein the ratio of the number of microwells containing 2 or more cells divided by the number of microwells containing a single cell is less than 20%.
• each microwell has a volume between 1 picoliter and 500 nanoliters; b) said microwells occupy a density greater than 100 wells per cm 2 ; c) said microwells are intermittently accessible to external reagents; d) oligonucleotides are attached to surfaces inside said microwells; e) said oligonucleotides contain less than 100 sequences complementary to mRNA coding for said cis- and/or trans-protein complexes; and f) said oligonucleotides contain one or more unique tags common to all identical oligonucleotides within the same microwell.
• the invention further comprises lysing said cells, optionally capturing said cis- and/or trans-protein complexes on surfaces inside said microwells, subjecting said cis- and/or trans-protein complexes to differing concentrations of fluorescently labeled ligands, and measuring the decrease in fluorescence over time, capturing said mRNA by hybridizing them to said oligonucleotides, converting said captured mRNA to cDNA, pooling said cDNA and sequencing them, and digitally reconstructing said structure of said cis- and/or trans-protein complexes from the cDNA sequences associate with each cell.
• FIG. 1 is a schematic representation of a B cell or plasma cell captured in a micro- well.
• FIG. 2 is a flowchart of a methodology which could be used in connection with the multi-well system of the present invention.
• FIG. 3 is a schematic representation of mRNA capture and subsequent conversion into tagged cDNA.
• FIG. 4 depicts the features of 2 oligonucleotide probes for capturing mRNA from antibody-producing cells, one for the mouse heavy chain (top) (SEQ ID NO: 1) and one for mouse light chain (bottom) (SEQ ID NO:2).
• 401 and 406 are a recognition site used for cleaving the synthesized cDNA off the microarray by the endonuclease Xhol.
• 402 and 406 are the primer sequence to be used for PCR amplification.
• 403 and 408 are landmark dinucleotides to enhance distinction between the PCR primer and the unique 14-nucleotide tag containing the error- correcting Hamming codes denoted by Ns (404 and 409).
• 405 is the oligo complementary to the mouse heavy chain mRNA constant region including isotypes 1, 2a, and 2b.
• 410 is the oligo complementary to the mouse kappa light chain mRNA. There is a spacer and 6 deoxyadenosine residues to get the capture oligo away from the surface of the microarray for better capture efficiency.
• FIG. 5 is a schematic view of an embodiment of a multi-well tray component
• the wells include indices or addresses 1-12 (2) along the row and indices or addresses A-H (3) along the columns providing a conventional 96 well tray.
• FIG. 6 is a schematic view of a multi-well tray top component which could be used in connection with the present invention.
• the top 4 is comprised of a basic frame 5 and includes a plurality of areas 6 on the top. Each area 6 is addressed with indices as in the multi-well tray 1 of FIG. 5. The areas are numbered 1-12 along the rows and A-H along the columns as with the tray of FIG. 5. Portions 14-17 are cut out to provide precise alignment with a top component in, for example, FIG. 7.
• FIG. 7 is a schematic view of a second embodiment of a multi-well tray component which could be used in connection with the top component of FIG. 6.
• the tray is comprised of a frame 8 which includes a plurality of wells 9.
• the tray includes upwardly extending notches 10, 1 1, 12 and 13 in each of the corners.
• the notches 10- 13 fit within the cut-out portions 14, 15, 16 and 17 of the top shown in FIG. 6. In this manner the top and the tray can be precisely aligned with each other.
• FIG. 8 is a schematic view of a second embodiment of the top which is shown in FIG. 6 wherein the top includes a protuberance on each of the areas.
• Tray top 20 comprised of a frame 21 and protuberances 22 on each of the areas corresponding to the well 3 of FIG. 5.
• each area includes a single protuberance.
• the area may include 2, 3, 4 or any greater number of protuberances.
• FIG. 9 is an exploded schematic view of a system of the invention showing specific components for aligning the tray with tray tops.
• FIG. 10 is a schematic view of micro-wells with different designs and configurations 601-608, which may provide local addressability when the field of view does not encompass all micro-wells.
• oligonucleotide tag(s) refer to an oligonucleotide whose sequence identifies the physical location of its origin.
• oligonucleotide includes linear oligomers of natural or modified monomers or linkages, including deoxyribonucleosides, ribonucleosides, anomeric forms thereof, peptide nucleic acids (PNAs), and the like, capable of specifically binding to a target polynucleotide by way of a regular pattern of monomer-to-monomer interactions, such as Watson-Crick type of base pairing, base stacking, Hoogsteen or reverse Hoogsteen types of base pairing, or the like.
• oligonucleotides ranging in size from a few monomeric units, e.g. 3-4, to several tens of monomeric units, e.g. 40-60.
• ATGCCTG an oligonucleotide is represented by a sequence of letters, such as "ATGCCTG,” it will be understood that the nucleotides are in 5'. -.3' order from left to right and that "A” denotes deoxyadenosine, "C” denotes deoxycytidine, “G” denotes deoxyguanosine, and "T” denotes thymidine, unless otherwise noted.
• oligonucleotides of the invention comprise the four natural nucleotides; however, they may also comprise non-natural nucleotide analogs. It is clear to those skilled in the art when oligonucleotides having natural or non-natural nucleotides may be employed, e.g. where processing by enzymes is called for, usually oligonucleotides consisting of natural nucleotides are required.
• Perfectly matched in reference to a duplex means that the poly- or oligonucleotide strands making up the duplex form a double stranded structure with one other such that every nucleotide in each strand undergoes Watson-Crick basepairing with a nucleotide in the other strand.
• the term also comprehends the pairing of nucleoside analogs, such as deoxyinosine, nucleosides with 2-aminopurine bases, and the like, that may be employed.
• the term means that the triplex consists of a perfectly matched duplex and a third strand in which every nucleotide undergoes Hoogsteen or reverse Hoogsteen association with a basepair of the perfectly matched duplex.
• a "mismatch" in a duplex between a tag and an oligonucleotide means that a pair or triplet of nucleotides in the duplex or triplex fails to undergo Watson-Crick and/or Hoogsteen and/or reverse Hoogsteen bonding.
• nucleoside includes the natural nucleosides, including T- deoxy and 2'-hydroxyl forms, e.g. as described in Kornberg and Baker, DNA Replication, 2nd Ed. (Freeman, San Francisco, 1992).
• "Analogs” in reference to nucleosides includes synthetic nucleosides having modified base moieties and/or modified sugar moieties, e.g. described by Scheit, Nucleotide Analogs (John Wiley, New York, 1980); Uhlman and Peyman, Chemical Reviews 90:543-584 (1990), or the like, with the only proviso that they are capable of specific hybridization.
• Such analogs include synthetic nucleosides designed to enhance binding properties, reduce complexity, increase specificity, and the like.
• sequence determination or "determining a nucleotide sequence” in reference to polynucleotides includes determination of partial as well as full sequence information of the polynucleotide. That is, the term includes sequence comparisons, fingerprinting, and like levels of information about a target polynucleotide, as well as the express identification and ordering of nucleosides, usually each nucleoside, in a target polynucleotide. The term also includes the determination of the identification, ordering, and locations of one, two, or three of the four types of nucleotides within a target polynucleotide.
• epitope is the part of a macromolecule that is recognized by the immune system, specifically by antibodies, B cells, or T cells. Although epitopes are usually thought to be derived from nonself proteins, sequences derived from the host that can be recognized are also classified as epitopes. Most epitopes recognized by antibodies or B cells can be thought of as three-dimensional surface features of an antigen molecule; these features fit precisely and thus bind to antibodies.
• hybridization refers to the process wherein cellular RNA or single stranded DNA interacts with oligonucleotides having substantial sequence complementariy, wherein duplexes are formed in said regions of sequence complementarity.
• microwell refers to sub millimeter structures with a volume between 1 picoliter and 500 nanoliters.
• the microwell is typically constructed in a shape that allows dense packing on a planar substrate, i.e.: the shape is triangular, rectangular, or hexagonal. Microwells can be either opened by removing one surface, usually at the top, or closed by placing said top in contact with other surfaces.
• the microwell can be homogeneous, or constructed out of dissimilar materials, including but not limited to glass, photoresist, or polydimethylsiloxane (PDMS).
• PDMS polydimethylsiloxane
• paratope refers to the part of an antibody that recognizes the epitope of an antigen.
• phOX refers to 4- ⁇ [(Z)-(5-OXO-2-PHENYL-l ,3-
• rotamers refer to low energy side-chain conformations.
• the use of a build-library of rotamers allows anyone determining or modeling a structure to try the most likely side-chain conformations, saving time and producing a structure that is more likely to be correct. This is, of course, only the case if the rotamers really are the correct low energy conformations.
• Libraries address this quality issue in a number of ways: they use only very high resolution structures (1.8 A or better), remove side chains whose position may be in doubt using a number of filters, use the mode rather than the mean of observed conformations (which has a number of advantages), and make efforts to remove systematically misfit conformations.
• mutants are changes to the nucleotide sequence of the genetic material of an organism. Mutations can be caused by copying errors in the genetic material during cell division, by exposure to ultraviolet or ionizing radiation, chemical mutagens, or viruses, or can occur deliberately under cellular control during processes such as hypermutation. In multicellular organisms, mutations can be subdivided into germ line mutations, which can be passed on to descendants, and, as used herein, "somatic mutations", which cannot be transmitted to descendants in animals. B cells undergo somatic mutations during the process of affinity maturation.
• structure refers to four distinct aspects of a protein's structure: a) the primary structure is the amino acid sequence of the peptide chains, b) the secondary structure is the highly regular sub-structures (alpha helix and strands of beta sheet) which are locally defined, meaning that there can be many different secondary motifs present in one single protein molecule, c) tertiary structure is the three-dimensional structure of a single protein molecule; a spatial arrangement of the secondary structures, and d) the quaternary structure is the complex of several protein molecules or polypeptide chains, usually called protein subunits in this context, which function as part of the larger assembly or protein complex.
• Capture agent is a molecule used to immobilize a cis protein complex.
• Capture agents can be oligonucleotides, DNA, RNA, protein, small molecules, peptides, aptamers, etc which have an affinity for their respective natural or artificial ligands.
• the term "monoclonal antibody” relates to an antibody chosen from a mixture of different antibodies. All monoclonal antibodies of the same specificity are identical except for natural mutants thereof. Under the term “antibody” intact molecules of immunoglobulins as well as fragments thereof (Fab, F(ab'), Fv, scFv) are to be understood.
• a "ligand” is a substance that is able to bind to and form a complex with a biomolecule to serve a biological purpose.
• B cell is used herein to mean an immune cell that develops in the bone marrow and is highly specialized for making immunoglobins and antibodies.
• a B cell is a lymphocyte which is derived from bone marrow and provides humoral immunity.
• a B cell recognizes antigen molecules in solution and matures into a plasma cell.
• B cell is intended to encompass cells developed from B cells such as plasma cells.
• plasma cell is intended to mean a cell that develops from a B lymphocyte in reaction to a specific antigen. Plasma cells are found in bone marrow and blood. A plasma cell may also be called a plasma B cell or plasmacyte and are cells in the immune system which secrete large amounts of antibodies. Plasma cells differentiate from B cells upon stimulation by CD4+ lymphocytes. A plasma cell is a type of white blood cell that produces antibodies and is derived from an antigen- specific B cell. Throughout this application the term "B cell” is intended to encompass “plasma cells” and vice versa. In general both are intended to encompass terms referring to cells which produce antibodies of interest.
• antibodies are characterized by their "binding affinity" to a given binding site or epitope. Every antibody is comprised of a particular 3 -dimensional structure of amino acids, which binds to another structure referred to as an epitope or antigen.
• binding affinity is measured by the ratio of complexed to free reactants at equilibrium. The lower the concentration of the reactants at equilibrium, the higher the binding affinity of the antibody for the antigen.
• affinity constant is represented by the symbol "K” or sometimes referred to as "Ka”.
• K is defined by the equation II as follows:
• brackets denote concentration in moles per liter or liters per mole.
• a typical value for the binding affinity Ka which is also referred to as "K” and is the "affinity constant" which for a typical antibody is in a range of from about 10 5 to about 10 1 ' liters per mole.
• the Ka is the concentration of free antigen needed to fill half the binding sites of the antibody present in solution with the antigen. If measured in liters per mole a higher Ka (e.g. 10 1 ') or higher affinity constant indicates a large volume of solvent, a very dilute concentration of free antigen, and as such indicates the antibody has a high binding affinity for the epitope.
• a low Ka e.g. 10 "1 ' indicates a less concentrated solution of the free antigen needed to occupy half of the antibody binding sites, and as such a high binding affinity.
• Equation III the units for K are liters per mole. Typical values in liters per mole are in a range of from about 10 5 to about l ⁇ " liters per mole.
• K [Ag] where the units for K are in moles per liter, and the typical values are in a range of 10 ' " to 10 '5 moles per liter.
• binding affinities can vary over six orders of magnitude.
• what might be considered a useful antibody might have 100,000 times greater binding affinity as compared to the binding affinity of what might be considered a different antibody, which is also considered useful.
• binding characteristics of an antibody to an antigen can be defined using terminology and methods well defined in the field of immunology.
• the binding affinity or "K" of an antibody can be precisely determined.
• protein complex is used to refer to a group of two or more constituent proteins formed by protein-protein interactions that may or may not involve formation of covalent bonds. Protein complexes are a form of quaternary structure.
• An example is IgG, which is formed by a heavy chain and a light chain. In this case, there are disulfide linkages between the heavy and light chains. Protein complexes that are formed by constituent proteins deriving from the same cell are referred to as "cis protein complexes". As such, IgG is a perfect example of a cis protein complex.
• trans protein complexes that are formed by constituent proteins deriving from different cells or different origins are referred to as "trans protein complexes.”
• An example of a trans protein complex is an antibody-antigen complex.
• an antibody-antigen complex involves a nested cis protein complex.
• the present invention relates to both cis and trans protein complexes.
• kinetic properties refer to the rates of reaction k o ff, Ic 0n , and their ratio K D between cis and/or trans protein complexes.
• dissociation constant Kp is monotonically related to the Gibbs free energy which describes the work obtainable from an isothermal, isobaric process, conditions closely approximated in living systems.
• binding affinity does not necessarily translate to a highly effective drug.
• the candidates showing a wide range of binding affinities may be tested to determine if they obtain the desired biochemical/physiological response.
• binding affinity is important, some drug candidates with high binding affinity are not effective drugs and some drug candidates with low binding affinity are effective drugs.
• the present invention provides a method for characterizing molecular interactions within a single cell. Central to said method is the confinement of single cells into individual addressable microwells. Said microwells serve 2 purposes. One is to inhibit the diffusion of reactants and products among individual cells. Second is to accelerate rates for processes such as nucleic acid hybridization or protein interactions. Moreover, said microwell comprises capture agents that allow efficient capture of the intended macromolecules on a cell by cell basis.
• one or a plurality of capture agents each comprise a tag unique to the addressable microwell where a single cell is confined.
• the target macromolecules can be captured rapidly.
• the means for confinement may optionally be removed to allow manipulation of the captured macromolecules and/or measurement of kinetic properties of the interactions between the captured macromolecules and a labeled ligand.
• the captured macromolecules such as mRNA can be converted into double stranded (ds) cDNA incorporating said tag identifying its originating microwell. Said ds cDNA can then be aggregated and processed by massively parallel single-molecule based DNA sequencing technology.
• microwell identifying tags are converted into digital tags in the form of a DNA sequence. Said digital tags can then be used to identify and cluster the primary structure of the distinct constituent macromolecules as part of a cis or trans protein complex originating from a single cell.
• a microarray reader When fluorescent measurements are taken, of cells or surface bound antibodies, a microarray reader produces an image wherein the intensity of various pixels must be associated with the concentration of cell surface markers, or surface bound antibodies, in specific wells. To insure proper registration between the confined cell, the captured mRNA, and optionally the captured protein, it is desirable to include marker cells with a known cis protein complex into the cell population under investigation.
• the system can be tested using a hybridoma cell line that is optionally capable of expressing membrane bound antibody with known sequence information for both heavy and light chain.
• a hybridoma cell line that is optionally capable of expressing membrane bound antibody with known sequence information for both heavy and light chain.
• Such lines are deposited and described in the literature and easily acquired.
• These cells can be stained with an antigen labeled with a distinct fluorophore so they can be identified in the addressable microwells.
• their respective mRNA will be processed and sequenced so the DNA sequence plus the digital tags will positively identify the position of the marker cells on the capture microarray slide.
• the antibody captured on the array can also be stained with the appropriate antigen with the distinct dye to identify its position on the protein array.
• the position of the marker cells on the microarray slide can be matched with those on the protein array.
• the mRNA and protein of other cells in the array can be matched based on their position relative to the marker cells, their mRNA and antibodies.
• One embodiment of the method of the invention comprises a method of obtaining information from a plurality of isolated cells.
• the information may be simultaneously obtained from a large number of cells by placing the large number of cells in individual wells. An attempt is made to include a single cell within a single well. However, when carrying out the method involving hundreds, thousands or even tens of thousands of cells and wells it may be that some wells do not include a cell and other wells include more than one cell.
• a method of the present invention may begin with immunizing an animal and extracting antibody producing cells from that animal. However, the process may begin with the cells already having been extracted and placing the cells into wells of a well tray.
• a well tray comprised of microwells is used. The microwells have a volume sufficient to accommodate a single cell and liquid nutrient to support the cell for a limited period of time during which the cell produces antibodies.
• the invention can be carried out when only a small percentage of the microwells contain a single cell, e.g. 1%, 5%, 10%, 50% or more of the cells only contain a single cell and the remainder of the wells contain no cell or a plurality of cells, i.e. 2 or more cells. It is desirable if a very high percentage, 70% or more, 80% or more, 90% or more, or 95% or more of the wells contain a single cell and only a single cell. This makes it possible to utilize all of the wells and specifically relate antibodies produced in the well to a single cell.
• the invention that can be carried out when a relatively small number of the cells are actually producing antibodies. For example, it may be that only 1%, 5%, 10% or 50% of the cells in the wells are actually producing antibodies in detectable amounts even though it is desirable to obtain a high percentage of antibody producing cells, e.g. 70% or more, 80% or more, 90% or more, or 95% or more of the cells placed in wells are producing antibodies. The more wells containing a single cell which is producing antibodies the greater the efficiency of the methodology of the invention.
• the cells are cells such as B cells or plasma cells which produce antibodies and the antibodies which are produced in the wells are brought into contact with a binding agent such as protein A which is bound to a surface which may be a membrane.
• a binding agent such as protein A which is bound to a surface which may be a membrane.
• This surface may have a plurality of addressable regions or will include regions which can be specifically relatable to individual wells.
• the wells may be in a well tray which has a well density of 100 or more wells per cm 2 or 1,000 or more wells per cm 2 and the wells may include a detectable marker which makes it possible to determine the position of a particular well relative to other wells and the marker may be a marker cell or a group of markers which could include a dye, a nucleotide sequence, a radioactive label or a quantum dot.
• binding information relating to the binding of the antibodies which are bound to the surface is then associated with the particular well in which the antibodies were obtained.
• RNA obtained from particular wells of interest may be obtained by binding messenger RNA in the wells to sequences which selectively bind to sequences which encode antibodies such as sequences which encode light and heavy chains of antibodies.
• the messenger RNA obtained can be converted to cDNA.
• the cDNA may contain tags which are specific to the well of particular interest.
• the tag may be used to associate binding information relating to antibodies of particular interest with messenger RNA from wells of particular interest.
• Microwell 101 of Figure 1 may have dimensions 50 microns by 50 microns by
• Dimensions 105 measure 0 to 50 microns from the bottom of microwell
• a plasmocyte 102 is suspended inside microwell 101 in a buffered solution that fills the entire microwell.
• DNA oligonucleotides are attached to the bottom surface of microwell 101 in contiguous areas called pads.
• Pad 103 contains an oligonucleotide complementary to an invariant sequence in the mRNA of plasmocyte 102 that codes for the heavy chain of an antibody.
• Pad 104 contains an oligonucleotide complementary to an invariant sequence in the mRNA of plasmocyte
• microwell 101 that codes for the light chain of an antibody. Said invariant sequences are selected so they will bind strongly and physically capture complementary mRNA when said mRNA is released from plasmocyte 102 and diffuses into the solution which may be a cell culture solution in microwell 101. Whereas microwell 101 will function properly in any orientation, for the purposes of illustration in Fig. 1 pad 103 and pad 104 are shown attached to the bottom of microwell 101.
• the macromolecules to be analyzed are antibodies produced by cells in a host as an immune response of that host to an antigen.
• the combination of the antibody's heavy and light chain primary structure can be determined for each cell analyzed e.g.
• the present invention can be applied to antibodies produced by animals with the ability to generate a humoral immune response.
• a prerequisite for practicing the present invention is the knowledge of the sequence of the constant region for the heavy and light chain mRNA of an antibody for a given isotype. Since the present invention obtains mRNA and proteins directly from antibody producing cells such as B cells, it clearly obviates the need for cell fusion to generate hybridoma cells.
• the present invention can be used to follow an immune response by taking antibody producing cells such as plasma cells and/or antigen specific B cells from any day after immunization. Furthermore, the present invention can be used to monitor the state of the immune system by profiling the B cell population without selection from mouse spleen or even those B cells in circulation for a human subject. This could be very useful in studying autoimmune diseases and to discover biomarkers or potential drug targets. Certainly, the T cell receptors having a structure similar to antibodies can be analyzed in a similar fashion for studying immune functions.
• mouse IgGl , IgG2a, and IgG2b isotype heavy chain conserved sequence and the K light chain sequence are used for capturing the mouse antibody mRNA in the example illustrated, this represents an embodiment rather than a limitation of the invention. It is entirely within the scope of the present invention to use spotted microarrays wherein a mixture of oligonucleotide probes comprising appropriate sequences can be attached and used to capture all isotypes.
• the frequency of occurrence for a given antibody sequence can be used to estimate the K D of that antibody due to the phenomenon of clonal selection during an immune response.
• This estimated K D can be correlated with the measured value obtained from captured antibodies.
• the present invention can be leveraged to screen constructs in many display technologies, such as yeast display, bacterial display, and mammalian display.
• the candidate display clones can be enriched from the library analogous to the manner for selecting antigen specific B cells by flow cytometry. Once enriched, these display clones can be separated into micro wells just like antigen specific B cells and processed in a very similar way. A change in the capture sequence has to be made appropriate for the display technology used.
• the present invention can be used to investigate cis protein complexes in other cell types.
• many cell surface receptors responsible for signal transduction possess the ability to form cis complexes with other receptors via non- covalent bonds. It is conceivable to use the present invention to examine these receptors and identify qualitative changes on a per cell basis. In this case, characteristics, such as morphology, surface marker expression, or intracellular marker expression, can be recorded on a per cell basis to be correlated with the sequence information for the receptors under investigation. A cell-by-cell comparison between normal and cancer cells can be envisioned.
• Rare cell populations such as stem cells, can also be analyzed using the present invention to relate candidate macromolecules with the observed phenotypes on a per cell basis.
• the present invention estimates the free binding energy of the antibody and the putative protein folding. With the potential epitope identified for each antibody, this provides another criterion to classify the antibody obtained for a target antigen.
• the ability to quickly identify sets of antibodies each against different epitopes on an antigen is an advantage of the invention. This reduces the number of confirmatory tests required given the large number of different antibodies recovered. Deciphering the structures local to the identified epitopes on the antigen can lead to a good understanding of the overall structure of the antigen when the density of the epitope identified becomes high enough. This outcome is also unprecedented. These are all due to the fact that a large number of antibodies can be rapidly recovered using the invention.
• Microwells may be produced by attaching 50 micron ( ⁇ 25%) high walls onto a flat support and binding oligonucleotides pads inside the wells. Cells are distributed over these microwells in such a manner that it allows a single cell to settle into a microwell. A cover that is coated with a material suitable for attaching proteins of interest is placed over said microwells. For example, to immobilize antibodies on the top cover the cover is coated with an antibody specific capture agent such as Protein A or Protein L (Sigma-Aldrich, St. Louis, MO).
• an antibody specific capture agent such as Protein A or Protein L (Sigma-Aldrich, St. Louis, MO).
• a material suitable for attaching proteins of interest is coated on a commercial microwell array, e.g.: a blank PicoTiterPlate device (454 Life Sciences, Branford, Connecticut) containing 50 micron hexagonal wells. Cells are distributed over said hexagonal wells in such a manner that allows a single cell to settle into a well. For example, to immobilize antibodies on the surfaces of the wells one coats the surfaces with an antibody specific compound such as Protein A. A custom oligonucleotide array (NimbleGen Systems, Inc., Madison, Wisconsin) is placed over said PicoTiterPlate to capture and tag mRNAs.
• a commercial microwell array e.g.: a blank PicoTiterPlate device (454 Life Sciences, Branford, Connecticut) containing 50 micron hexagonal wells. Cells are distributed over said hexagonal wells in such a manner that allows a single cell to settle into a well.
• an antibody specific compound such as Protein A.
• microwells by attaching approximately 50 micron walls onto a flat support. Cells are distributed over said microwells in such a manner that allows a single cell to settle into a microwell. A custom oligonucleotide array (NimbleGen Systems, Inc., Madison, Wisconsin) is placed over said fabricated microwells in order to capture and tag mRNAs. No proteins are captured.
• PicoTiterPlate device (454 Life Sciences, Branford, Connecticut) containing 50 micron hexagonal wells, is used to contain the distributed cells.
• a custom oligonucleotide array (NimbleGen Systems, Inc., Madison, Wisconsin) is placed over said commercial microwell array to capture and tag mRNAs. No proteins are captured.
• two planar surfaces are separated a small distance (e.g.: 50 microns) by a porous structure.
• One or both planar surfaces are microarrays.
• the porous structure contains holes large enough to contain a biological cell (e.g.: 50 microns).
• the porous structure is temporarily affixed to one planar surface, thereby constructing an array of open microwells.
• Biological cells are dispersed over the top of said microwells in one of two methods: a) stochastic separation, wherein a concentration of said cells is chosen so that only a single cell usually occupies a single microwell when the cells are randomly dispersed above said microwells; and b) deterministic separation, wherein individual cells are caused to move to predetermined microwells.
• microwells After a period of time (e.g.: 3 minutes) cells above microwells are allowed to enter said microwells due to their increased density. Reagents common to all microwells are introduced to the region above said microwells and reactions occur within each microwell. Small molecules are allowed to diffuse out of said microwells in a short amount of time (e.g.: 10 seconds). Then the second planar surface is placed over said microwells sealing them and allowing reactions inside the microwells to occur over a longer period of time. Said reactions result in a modification of the microarray(s) by chemicals confined to said microwells. After said microarray(s) are deemed modified, the planar arrays are separated and the porous structure removed.
• a period of time e.g.: 3 minutes
• Codes fabricated into said modified microarray(s) are used during analysis to associate microwells with measured results.
• Said codes may be the physical position on a microarray, or a tag caused to be embedded in the analyzed data.
• said embedded tag may be a unique DNA sequence.
• the invention includes a device, system and/or kit which can be used in carrying out the methodology of the invention.
• a specific multi-well system can be designed which is comprised of a tray comprising a plurality of wells. Each of the wells is comprised of a side wall, a bottom and an open top.
• the tray may include any number of wells and preferably includes 96 or more wells, 100, 1,000, 10,000, 100,000, 1 ,000,000 wells or more.
• the wells are designed so that they are capable of holding a single cell and the tray surface is designed such that when the cells are placed on and moved about the surface of the tray a single cell is moved into each of the wells.
• the system includes a tray top which is comprised of a plurality of areas wherein each of the area corresponds uniquely with each well on the tray.
• the areas may be planar or protrude outward to provide more surface area.
• the areas (and optional protuberances) on the tray top are coated with an antibody binding agent such as protein A, protein G, protein L, protein A/G and/or goat anti-mouse IgG antibodies.
• the coating can include any agent which efficiently and selectively binds to antibodies which are in the well.
• Each of the wells may also have coated thereon a polynucleotide, e.g. an oligonucleotide.
• the polynucleotide may act as a primer to replicate nucleotides in the well after the cells are lysed, for example, in a sequencing reaction.
• the device may be in a kit that includes instructions to use the device in accordance with any method described here. Further, the device may be sold with reagents including PCR reagents.
• Example 1 Acquisition of both the heavy and light chain sequence for mouse anti-HEL antibodies
• a group of BALB/c mice 201 are immunized intraperitoneally with 50 ⁇ g of hen egg lysozyme (HEL, Sigma, St. Louis, MO) in complete Freund's adjuvant (Sigma).
• HEL hen egg lysozyme
• the mice are immunized intravenously with the same dose of HEL.
• blood is taken from the tail vein of the mice and the presence of polyclonal antibodies against HEL in the sera is determined by an ELISA test. If the titer determined by said ELISA test is satisfactory, the mice are sacrificed the next day and their spleens harvested.
• Cell suspensions of splenocytes are obtained by mechanical disruption of the spleens, and erythrocytes are lysed in 0.16 M chloride ammonium solution at pH 7.4.
• the resulting single-cell suspensions are stained with a combination of HEL labeled with FITC (Pierce Biotechnology, Inc., Rockford, IL) and HEL labeled with PE-Cy5 (Prozyme, San Leandro, CA) at optimal dilution. Staining is conducted at 4°C in 2 steps. First, cells are stained with the FITC-labeled HEL for one hour, using the empirically determined optimal sub-saturating concentration. Cells are then washed three times with FACS buffer. Next, cells are stained with the PE-Cy5 labeled HEL. After staining, cells are washed twice in PBS with 5% FCS.
• step 202 single B cells with appropriate surface phenotype are sorted for repertoire analysis using the automatic cell-dispensing unit attached to the FAC-Star PLUS TM and Clone-Cyt software (Becton Dickinson). Cells are sorted into an appropriate volume of PBS supplemented with an RNase inhibitor, SUPERase-In, at a concentration of 1 U/ ⁇ L.
• antigen-specific B cells can be isolated using magnetic-assisted cell sorting (MACS) using reagents identifying appropriate cell surface markers.
• MCS magnetic-assisted cell sorting
• antigen-specific B cells can be isolated by agarose gel microdrops using a CellSys 101 microdrop maker (One Cell Systems, Inc., Cambridge, MA, USA) or microdroplets resulting from water-in-oil emulsion.
• a combination of the methods mentioned thereof can be used to isolate antigen-specific B cells.
• a PicoTiterPlate (PTP) device (454 Life Sciences, Branford, CT) is prepared and the surface coated with Protein L (Pierce Biotechnology, Inc., Rockford, IL) in 0.1 M sodium acetate overnight. The surface is blocked with 3% BSA in PBS for 1 hour. After removing 3% BSA in PBS, the surface is washed 4 times with 0.1% Tween-20 in PBS. The PTP device is then filled with PBS supplemented with SUPERase-In. Air bubbles that might remain in the wells are dislodged by centrifugation, once the PTP device is in the Bead Deposition Device (454 Life Sciences, Branford, CT).
• PTP PicoTiterPlate
• a 2-mL pipette Using a 2-mL pipette, cells are gently placed on top of the PTP device and let sit for 10 minutes to allow individual cell to fall into a well. Cells that do not go into a well are moved off the PTP device with a coverslip. Cells are lysed with a customary lysing solution including a chaotropic agent such as guanidinium thiocyanate or a detergent such as NP-40 (step 204). If capturing of the protein of interest is desired, the detergent NP-40 is to be used.
• a chaotropic agent such as guanidinium thiocyanate
• a detergent such as NP-40
• a solid surface coated with a capture agent such as protein A or protein L is used to cover the micro wells to confine diffusion of macromolecules released from the lysed single cell and to simultaneously capture said proteins of interest such as antibodies on the solid surface forming a protein array (step 211).
• Arrays of cylindrical posts of photoresist are fabricated on silicon wafers using standard photolithographic techniques and rigid chrome masks.
• the arrays of square features measuring 50 ⁇ m x 50 ⁇ m x 50 ⁇ m with the inter-feature spacing of 50 ⁇ m are fabricated using transparencies as photomasks.
• the PDMS prepolymer (mix in a 10: 1 ratio with a crosslinking catalyst) is spin-coated on the bas-relief of patterned photoresist features mentioned above at 3,000 rpm for 60 second to generate a film that is ca. 45 ⁇ m thick.
• the resulting PDMS membrane possesses square holes defined by the dimension of the photoresist features.
• the PDMS membranes are cured for 2 h at 6O 0 C.
• a thicker layer of PDMS prepolymer is added to the edges of the membranes in dropwise fashion.
• the membranes are kept at 60 0 C overnight.
• the membranes are removed from their supports using tweezers and are cut to the desired sizes along the edges of the support.
• the PDMS membranes are placed on the surface of a glass slide with a few drops of ethanol. Drops of a buffered solution of BSA (1% w/v, in PBS) are placed on the membrane to cover the holes. Since the fluid does not readily fill the hydrophobic pores, a vacuum (ca. 500 mTorr) is applied for 30 seconds and released twice to extract the air trapped in the holes and the BSA is allowed to adsorb to the surfaces for 15 min. The PDMS membranes on the glass slides are then rinsed three times with PBS. The membranes are peeled from the glass slide in the presence of PBS and transferred to a protein array slide (Full Moon BioSystems, Sunnyvale, CA) covered with PBS to help seal the membrane onto the slide.
• BSA 1% w/v, in PBS
• the NimbleGen HD-2 microarray chips have 2.1 million probes on a single slide with the array size of 62 mm x 14 mm. As such, there is a potential to have 2.1 million unique tags.
• general features of a probe for both heavy chain and light chain are utilized wherein an example of said general features for a heavy chain capture probe are: Xhol cleavage, Primer B by 454 Life Sciences, a 2-base Spacer (always constant) to identify the start of the well identifier tag, a 14 mer well identifier, a mouse gamma heavy chain CHl IgGl, IgG2a, and an IgG2b isotype heavy chain conserved sequence capture probe.
• an example of said general features for a light chain capture probe are an Xhol cleavage site, Primer A by 454 Life Sciences 407, a 2-base spacer (always constant) to identify the start of the well identifier tag, a 14 mer well identifier tag, and a mouse kappa light chain constant region capture probe.
• the length of the microwell identifier tag is a 14-mer, which has a possible sequence combination of over 268 million, far in excess of what is need for 2.1 million probes. This cushion allows elimination of undesirable sequences such as consecutive triples of the same base and perfect self-complementarity or complementarity between the microwell identifier and heavy chain probe sequence, light chain probe sequence, 454 primer A, or 454 primer.
• a parity code such as one used in Hamming codes, can be embedded in the well identifier for error-correction purposes.
• Examples of probes for immunoglobulin heavy chain (SEQ ID NO:1) and light chain (SEQ ID NO:2) polypeptides may be found in Figure 4. ] The process of capturing released mRNA from lysed cells and conversion into a tagged ds cDNA is illustrated in Fig. 3.
• a target molecule of mRNA 301 hybridizes to an oligonucleotide probe 203, which is attached to solid surface 306 as in a typical microarray slide comprising non-DNA linker 305, PCR/sequencing primer B of 454 Life Sciences 304, a well identifier tag 303, a capture oligonucleotide 302 complementary to a region in the target mRNA from either the heavy or light chain gene.
• Reverse transcription 307 uses a reverse transcriptase (Stratagene, La Jolla, CA) to synthesize the first strand cDNA 308 by extending the capture oligonucleotide 203 as a primer and copying an appropriate region of the target mRNA template thereby incorporating 5 '-methyl dCTP 309.
• Second strand cDNA reaction 310 replaces the target mRNA by a combined action of RNaseH and E. coli DNA polymerase I, leaving behind a small segment of the original mRNA template at the 5' end.
• Reaction 313 using T4 DNA polymerase blunts the 5' end of the ds cDNA 314.
• an adaptor molecule 316 comprising PCR/sequencing primer A of 454 Life Sciences with a 3' protruding end to insure orientation specific ligation is attached.
• excess adaptor molecules are removed and in process 319, the attached ds cDNA is cleaved off the solid surface by endonuclease Xhol (New England Biolabs, Ipswich, MA), releasing the ds cDNA molecule 320 with the well identifier tag flanked by 454 Life Sciences' s PCR/sequencing primers A and B ready to be plugged into the 454 sequencing workflow.
• NP-40 1% NP-40 is pipetted from one side of the PTP device to make the final NP-40 concentration at 0.5%.
• the PTP device is incubated for 10 seconds.
• the top of the PTP device is then covered with the NimbleGen HD-2 microarray chip, which is securely clamped down using an appropriate device. Incubate at 37°C for 30 minutes.
• the entire setup is then soaked in RNase free PBS held in a tray to separate the microarray from the PTP device. Wash the PTP device extensively with PBS for 3 times.
• PTP device now having the antibodies captured from single B cells can be stored at 4°C.
• the microarray was soaked in PBS held in a tray at 60°C for 10 minutes to remove non-specifically hybridized RNA species, then extensively washed with PBS for 3 times. The microarray is now ready for downstream manipulation.
• the microarray is briefly blotted dry on a piece of kimwipe and 30 ⁇ L of reverse transcriptase (RTase) reaction solution containing SuperScriptIII RTase (Invitrogen, Carlsbad, CA), appropriate buffer components, and dNTPs except 5'- methy dCTP is immediately added.
• RTase reverse transcriptase
• SuperScriptIII RTase Invitrogen, Carlsbad, CA
• dNTPs 5'- methy dCTP
• coli DNA polymerase and RNaseH is added, and the samples incubated at 16°C for 2 hours.
• the chip is washed and the synthesized double-stranded (ds) cDNA is polished by T4 DNA polymerase for 30 minutes at 37°C.
• Pre-annealed adaptors with a biotinylated end are added and ligated to blunt-ended cDNA on the chip by T4 DNA ligase at room temperature for 1 hour in an appropriate buffer. Excess adaptors are then removed by extensive washing in 10 mM Tris-HCl (pH 7.5), 0.1 mM EDTA.
• the slide with the cDNA attached can be stored at 4°C. [00128] Marker cells for registration between the DNA pads on the microarrav slide and the protein spots on the protein array
• hybridoma line TIB-228 American Type Culture Collection, Manassas,
• VA produces an antibody against human CD 14 with the isotype IgG2b.
• the DNA sequence has been determined for its heavy and light chains (GenBank accession number for heavy chain variable region and light chain variable region is AY669065 and AY669066, respectively).
• Recombinant human CD 14 can be obtained commercially (Abnova, Taipei, Taiwan).
• an appropriate number of cells in the range of 10 to 50, can be mixed with the enriched antigen-specific B prior to separating them into microwells.
• CD 14 can be labeled with PE-Cy5 to be distinguished from anti-HEL antibodies, which will be stained with FITC-labeled HEL.
• step 207 by incubating at 37°C for 15 minutes with Xhol endonucleases (New England Biolabs, Ipswich, MA).
• the released ds cDNA can be optionally captured by streptavidin beads (MyOne beads, Invitrogen, Carlsbad, CA) and stored. Such a strategy minimizes DNA loss during storage.
• the complementary strand can be melted off the beads and quantified using real time PCR by a 454 primer A and light chain primer with an appropriate probe located within the light chain region Similar reagents for real time PCR can be designed for the heavy chain ds cDNA.
• the ds cDNA is quantified, an appropriate amount is retrieved and mixed with appropriate amount of beads for subsequent emulsion PCR in step 208.
• the beads are processed and sequenced according to the vendor's recommendation (step 209). Including the spacer, the tag, the constant region, and the entire variable region, both the heavy and light chains require about 415 bases of sequence, which is within the limit of the 454 sequencing technology. Sequencing reads in one orientation are sufficient to obtain unambiguous sequence information to reconstruct the heavy and light chains for an antibody. This is because the genomic sequence of the prototype variable sequence is known. Furthermore, it is likely that FRl are mostly unmutated in the antibody sequence during immune response based on other reported sequences.
• the redundancy of the sequence reads per antibody is high.
• cDNA originating from specific wells identified by binding kinetics measurement can be directly amplified by incorporating a tag specific sequence at the 3 -end of the PCR primer.
• steps 210 and 213 After a sequencing run, the following steps are performed to analyze the sequence (steps 210 and 213): a) A list of sequences from a 454 run is obtained; b) The sequences are computationally evaluated and the tag, spacer, and constant region for each sequence identified, thereby determining whether each sequence is an H or L chain sequence.
• bases toward the 5' end of the heavy chain constant region are sequenced and the minute variation therein used to determined the isotype of the captured antibody; c) The constant region sequence and spacer are masked; d) The marker cell H and L chain sequence are identified; e) The tags corresponding to the marker cell H and L chain sequences are identified and examined to determine if they are in close proximity (i.e.: less than a microwell width) on the microarray. If affirmative, these tags identify a microwell.
• Locations of multiple microwells containing marker cells will establish the physical layout of the other microwells that each may contain a B cell; f) Based on the layout, a tag group for each expected microwell is generated; g) Sequences with identical H chain or L chain are identified; h) The corresponding tag for the identical H chain or L chain sequences are computationally evaluated. If the tags are identical, then the origin for that H chain or L chain is confirmed; i) Using the tags from confirmed H chains and confirmed L chains, the pairs of H tag and L tag are reviewed to see if they fit into expected tag groups. If affirmative, the combination is confirmed; j) Multiple H chain sequences or L chain sequences are aligned in a confirmed combination to obtain a consensus sequence.
• the consensus will be matched with the prototype genome sequences of the appropriate immunoglobuliln v genes; k) All CDRs and FRs on the paired H chain and L chain sequences are identified. In addition, identify mutated residues compared with the prototype; 1) Confirmed combinations are clustered and the frequency for identical combinations tallied to determine if they represent the outcome of a clonal selection event; and m) The DNA sequence is translated into amino acid sequence.
• the coverslip rotates at 500 rpm for 10 seconds and ramps up to 2,000 rpm over the next 30 seconds.
• the coverslip is soft baked for 20 minutes at 95 0 C and cools at room temperature for 10 minutes.
• An emulsion mask is designed using Adobe Photoshop and printed on a
• the mask is placed in contact with the SU-8 film, covered with a quartz slide to weight it down, and exposed in a Kasper 2001 Contact Mask Aligner for 1 minute at 365nm and at an intensity of approximately 200 mJ/cm 2 .
• the exposed photoresist is baked for 2 hours at 95°C on a level hotplate, soaked in PM Acetate for 30 minutes, and then cured at 200 0 C for 1 hour.
• the coated coverslip is soaked in sterile, distilled water overnight and sterilized in 70% ethanol in DI under a UV germicidal lamp for 1 hour.
• the cover slip is rinsed three times using sterile water and stored for at least 4 hours wet and ready for use. The 4 hour storage time ensures no gas bubbles remain in the wells.
• microwells comfortably contain a single 10-15 micron plasmocyte. Since the Reynold's number is 56 times the fluid velocity in meters/sec, there is no turbulent flow inside the wells. Therefore, once the wells are filled with fluid no gas bubbles enter them.
• This example refers to Embodiment 3 and Embodiment 4, above.
• GT guanidinium thiocyanate
• the number of GT molecules used in this simulation can scale to any convenient concentration. If we normalize to the concentration loaded above physical microwells, 21% will diffuse into microwells in 1.0 second, and 10 seconds after flushing the concentration above the microwells, the concentration inside the wells will fall to 0.65%. At time equal 11 seconds all mRNA is still completely contained within the wells. GT at this low concentration does not interfere with the hybridization of RNA to DNA, or DNA to DNA. The microwells are sealed after 11 seconds so that all mRNA continues to remain inside the microwells. [00143] The diffusivity was calculated from the Stokes-Einstein relation:
• D is the diffusivity
• kB is Boltzman's constant (1.38 x 10-23 J/K)
• T room temperature
• ⁇ is the viscosity of the buffer (8.94 x 10-4 Pa/sec)
• Example 4 Mapping antibody paratopes (step 214)
• the cis- and/or trans-protein complexes are antibodies
• our invention provides information about a much larger number of them than has previously been available.
• sequenced tags By associating the sequenced tags with the original microwells, we identify a population of mRNAs produced by B cells as well as their respective heavy and light chain sequence. Said sequences can infer the somatic mutations inside each B cells.
• n The most variable light and heavy chain amino acid are the most likely locations of the paratope.
• the paratope can be inferred because we can align a population of sequences.
• Our invention can also measure the K D of the antigen bound to the paratope, and we can plot the relationship between KD and probability of amino acid mutations.
• clusters in the KD -mutation graphs as evidence of significant immunological activity. When the immune system has found a stable heavy or light chain antibody structure small single-base mutations indicate that it can significantly improve specificity by mutating a single amino acid. Conversely, a single cluster with low K D indicates discovery of a successful somatic mutation. We strongly associate evidence of successful somatic mutations with paratopes.
• DEE Dead-End Elimination
• the present invention can computationally estimate the free binding energy of the antibody and the putative protein folding. To compute this energy estimate, we computationally dock the antibody with the putative protein. There are many methods of doing this, utilizing shape, electron density, or statistical frequencies. Large computing clusters significantly improve computation time. Typical run times on large computers run approximately 8 seconds per docking.
• Our invention compares the computational estimate of free binding energy to the measured KD and chooses the protein and epitope that most closely matches.
• the result of our invention is: a) a population of digitally immortalized antibodies against a specific antigen by obtaining the DNA sequences of their H and L chains; b) kinetic metrics of the interaction between each antibody and the antigen; c) computational mapping of the paratopes of each antibodies; d) computational mapping epitopes on the antigen; and e) modeling of the structure of the antigen aided by combining information from a), b), c) and d).
• Example 6 Inference of Kp from sequence frequencies and FACS fluorescence [00153] This example refers to Embodiment 3 and Embodiment 4.
• the surface of each B cell contains thousands of identical membrane bound B-CeIl Receptors (BCRs), and to a lesser extent plasmocytes do as well.
• BCRs B-CeIl Receptors
• We can specifically label them by subjecting the cells to a known concentration of fluorescently labeled antigen which will bind to a fraction of the BCRs, said fraction/ being closely approximated by the expression: f W
• K D is the dissociation constant and [a] is the concentration of antigen.
• the fraction/can be estimated by the fluorescence signal.
• large errors are introduced because cells vary in size.
• Estimates of /can be greatly improved by normalizing said fluorescent measurements by the size the of the cell, a dimension well correlated with forward scattered Fl signals from an appropriate cell sorting instrument, such as one from BD Biosciences, San Jose, CA. Reversing the above formula, since we know the concentration of antigen [a] used to label the cells, the KD can be estimated from the normalized fluorescent signals/as:
• Our invention distributes cells into micro wells and captures DNA complementary to mRNA on uniquely tagged oligonucleotides. It is ordinarily difficult to associate the K D inferred by FACS fluorescence with a tagged oligonucleotide since the cells are pooled prior to said distribution.
• the constant c is determined by: a) determining the number of times each sequence has been sampled; b) using an arbitrary value of c, computing the copy number associated with each sequence; c) sorting the sequences in order of said copy number; d) normalizing the side-scattered FACS signal F2 by the forward scattered FACS Fl signal to compute and estimate of the bound BCR surface density; e) sorting the FACS signals by said bound BCR density estimate; f) adjusting the parameter c to insure the total number of sequences equals the total number of FACS signals; g) aligning said sequences with said bound BCR density estimates; h) computing the K D for each said bound BCR density estimate; i) associating with each sequence the average Kp of said bound BCR density estimate aligned with said sequences.
• our invention distributes a certain number of cells over a surface populated by microwells. After a short time, e.g.: 3 minutes, said cells settle into the microwells. There is a competition between having as many microwells, and therefore as many cells, as possible, and leaving the microwells large enough that a) sufficient mRNA is captured by tagged oligonucleotides, and b) material from the cell's interior does not substantially interfere with mRNA-DNA hybridization.
• a 50 micron well size is a reasonable compromise.
• the well size may vary.
• microwells Once the size of the microwells is fixed, the number of microwells must be determined. A convenient dimension for the entire array is the size of a microscope cover slip, 34 * 34mm, of which only 24 * 24mm is used in order to allow room for mechanical support. This leaves room for 230 thousand microwells placed on 50 micron centers.
• Every microwell contains two tagged oligonucleotides to capture Ab mRNAs: one for the heavy chain and one for the light chain.
• two tagged oligonucleotides to capture Ab mRNAs In order to digitally associate these two sequences, at least one molecule from each well containing a cell must be sequenced. Since the cDNA sequences are released and pooled, we must over- sample the sequences to insure at least one sequence from the heavy and light chain of each cell are sequenced.
• the population of sequences is twice the number of cells.
• the probability p of selecting a particular heavy chain sequence equals the probability q of selecting the
• Example 9 Measuring k o /f and k on using fluorescence decrease (step 212) [00167]
• the hybridoma line (NQ2- 12.4) has a measured K D of 2.8 x 10 "7 molar "1 .
• Our invention takes advantage of the fact that tight binding K D s typically have k o ff values ⁇ 2.8 x 10 "2 sec "1 , and therefore easily allow the use of fluorescence to measure K D and k o f/in a 24x24mm antibody array.
• k on is computed k - k ° ff from " K D .
• our invention works for the extremely weak case of 2.8 x 10 '2 sec "1 and therefore will work for other commercially interesting antibodies.
• a microscope coverslip is coated with Protein A. Cells are distributed over the microwells, lysed, and said coverslip placed over the microwells.
• oligonucleotides are affixed to a surface inside the microwells. If a cells lysed in a microwell contains a large number of antibodies, these antibodies will diffuse throughout the well, into the vicinity of the Protein A and tightly bind, as is well known to those skilled in the art. After an incubation time commensurate with the anticipated range OfIc 0n and antibody concentration, the coverslip is removed, washed, and subjected to a solution of fluorescently labeled antigen.
• phOX antigen bound to NQ2-12.4 decreases quite quickly and represents one of the worst antibodies our invention anticipates measuring since its fluorescent decay time is the fastest we anticipate sampling. Tighter antibodies will have decay times orders of magnitude greater.
• the microarray reader will image approximately 230,000 antibody spots in approximately one minute and therefore infeasible to image all spots continuously or immediately. Our invention samples the signal decrease three times. Typical fluorescent measurements in digital numbers are: 736 in .39 seconds, 137 in 1.39 seconds, and 26 in 2.39 seconds.
• NimbleGen oligonucleotide arrays contain staggered oligonucleotide pads 13 microns x 13 microns in size. By staggered, it is meant alternating, for example, a chess board, wherein the black squares are staggered.
• PTP PicoTiterPlate
• Each well contained at least six pads. For each well we selected the six pads with the largest fractions, creating a 10,000 * 6 array. Considering this to be 10,000 samples of six numbers, the mean of the 6 fractions and their standard deviations, are: the first mean is 1 with a standard deviation of 0; the second mean in 0.99 with a standard deviation of 0.02; the third mean is 0.93 with a standard deviation of 0.07; the fourth mean is 0.81 with a standard deviation of 0.1 1; the fifth mean is 0.51 with a standard deviation of 0.15; and the sixth mean is 0.4 with a standard deviation of 0.15.
• Every well contained at least one complete pad. 99% contained at least 2 staggered pads. Therefore, our embodiment using NimbleGen oligonucleotide arrays and PTP hexagonal wells allows the heavy and light chains from 99% of the distributed cells to be digitally matched using DNA tags.
• Example 11 A glass slide coated with low melting point agarose.
• This method is useful when using a robotic microarray spotter (e.g.: SpotBot
• a 1% low melting point agarose (Invitrogen Corp., Carlsbad, CA) solution is dissolved in purified water and poured over the surface of a glass slides at 70°C (2.0 ml per slide). After gelling of the agarose, slides are dried in air. The dried slide is placed into the microarray spotting equipment and warm water (e.g.: 70°C) is dispensed onto the agarose. The agarose melts and is washed away with another application of warm water. A hole pattern is fabricated wherein said holes are as reproducible as the microarray spotter's tolerance (approximately 10% for SpotBot 2).
• the molecules coated onto the glass can be, for example, oligonucleotides, proteins, antibodies, or capture molecules, or a mixture of 2 or more oligonucleotides, proteins, antibodies, or capture molecules.
• One method of fabricating an oligonucleotide array complementary to mRNA utilizes synthesized oligonucleotides. This is difficult when considering arrays with, say, 40,000 or more oligonucleotides each with a unique tag.
• An efficient method of producing 40,000 oligonucleotides with unique tags comprises: a) Synthesizing 200 unique oligonucleotides without terminating phosphate groups; b) Synthesizing another 200 unique oligonucleotides with terminating phosphate groups; c) Ligating oligonucleotides from step (a) with oligonucleotides from step (b).
• oligonucleotides from step (a) cannot ligate with one another because of the missing phosphates.
• oligonucleotides from step (b) cannot ligate with one another because of the extra phosphates.
• d) Ligating the oligonucleotides from step (c) with the PCR primer.
• e) Ligating the oligonucleotides from step (d) with the region complementary to the mRNA.
• Example 12 Alignment between DNA chip and prefabricated wells
• SU-8 photoresist (MicroChem Corporation, Newton, MA, United States) was spin-coated onto a 10 cm silicon wafer wafer in accordance with manufacturer's recommendations.
• a pattern of 50 micron cubic micro-wells was exposed using ultraviolet light from a mask aligner (SUSS MicroTec AG, Garching, Germany) in accordance with manufacturer's recommendations and developed using SU-8 developer (MicroChem Corporation, Newton, MA, United States).
• PDMS Polydimethylsiloxane
• the bottom tray (FIG. 5) was formed by using a razor blade to cut out an array of 205 by 154 micro-wells (31, 570 micro- wells) and carefully placing it onto a clean and dry microscope slide where it formed a hydrophobic bond with the glass slide.
• the dimensions and location of the micro- wells exactly matched the location and size of pads of oligonucleotides on a DNA chip (385K CGH array, Roche/Nimblegen, Madison, WI, United States).
• the DNA chip formed the top of the micro-wells (FIG. 6) and was placed above the micro-wells so that most wells were directly beneath DNA and most well walls were in contact with bare glass. When micro-wells this small are used, the positioning, alignment, and subsequent sealing of a DNA slide above PDMS wells is sufficiently delicate that mechanical assistance is generally needed, such as a mask aligner or a custom built apparatus.
• One example of an available mask aligner is the MJB4 four inch manual mask aligner from SUSS MicroTec AG (Garching, Germany).
• a glass slide is affixed with mylar tape to a 4" square quartz plate and inserted into the aligner's mask vacuum chuck.
• PDMS is affixed to a similar plate and inserted into the wafer chuck.
• the two surfaces are aligned using optics and positioning controls available on the aligner. Once aligned, the PDMS is removed and processing continues until the DNA slide and wells must be aligned. At this time, the PDMS is reinserted into the aligner, the two surfaces (DNA and PDMS) are placed into contact, and the entire assembly is left alone for several minutes while cDNA is constructed from antibody mRNA.
• the system can be more efficiently used with a custom aligner designed to contain a small amount of fluid, provide easy access for the experimenter and equipment, while providing a reduced set of functions at a reduced cost.
• An example of a custom aligner 500 is shown in FIG. 9.
• Four vertical posts 502 screw into aluminum base plate 501 and support aluminum table 503.
• On aluminum table 503 sits the bottom pressure plate 504.
• a first plastic insert 505 and a second plastic insert 506 are sandwiched between bottom pressure plate 504 and top pressure plate 507.
• Vacuum port 508 provides close contact between bottom pressure plate 504 and plastic insert 505, as well as top pressure plate 507 and plastic insert 506.
• the bottom tray includes micro-wells 511 placed on glass microscope slide 510, and the tray is held firmly to the top side of plastic insert 505 by additional vacuum ports
• a small computer interfaced microscope (not shown) is positioned beneath the aluminum table 503 to image cells in wells using flat field light entering the top of apparatus 500.
• microwells 51 1 and the glass slide 510 can be removed, processed and returned to alignment apparatus 500 within a positional accuracy of 10 microns. It was found that 10 micron accuracy was adequate to correctly align the microwells 51 1 with the DNA chips 512 so that specific addresses on the chip 512 could be correctly matched to specific addresses of the microwells 511.
• Example 13 Embedding numeric codes in microwell design
• a coded shape such as a particular shape (FIG. 10) may be embedded into the wells.
• the shape is a tradeoff between three constraints: 1) the shapes should be different enough that epoxy coated wafers can easily reproduce them and, in turn, they can be seen in the PDMS impressions taken from the epoxy coated wafers; 2) the well volume should not be substantially different from well to well so that cells will experience approximately the same microenvironment; and 3) the wall thickness is not reduced in a manner which would weaken the PDMS structure. Fragments of an octagon provided a useful balance between these constraints. Octagon fragments were separated into symmetric or nonsymmetric fragments and used in shapes of FIG. 10.
• a 16 well block 600 is an example of the use of octagon fragments to embed three numbers in the shape of the wells: 1) the row number; 2) the column number; and 3) the pattern number.
• Binary representations are used to encode the row and column numbers. As is well known in computer literature, six binary digits are required to encode values 0 through 63.
• Symmetrical wells are used to represent row and column Is and 0s.
• well 605 is a 1
• well 607 is a zero.
• Nonsymmetrical wells are used at the corners of the block.
• Well 601 provides a starting point and starting direction.
• the other corners (602, 603 and 604) provide chirality, i.e. the shape is not identical to its mirror image in left and right handed microscopes images viewed from either the top or the bottom. Therefore, a method is needed to determine which wells go with which blocks without presupposing a particular viewing direction.
• the three corners of the block that are not the start well have a unique orientation that points into the center of the block.
• the two orientations can be used to represent a binary 1 (well 602) and a binary 0 (well 603) in order to encode additional information.
• well patterns each with a slightly different dimension so as to accommodate variations in PDMS shrinkage caused by different curing temperatures.
• the three corners encode for 8 different values, 0 through 7.
• FIG. 10 shows a block encoding the three values: column 3, row 4 and pattern
• the block is first located in a microscope's field of view by finding nonsymetrical well 601 which is designed to have the shape of a home-plate in baseball. Following four wells in the direction of well 601, well 602 defines the chirality of the block, in this case to the left. Wells 603 and 604 confirm this chirality. In addition, starting from the high bit, wells 604, 603 and 602 encode for the binary number 101 which, expressed in decimal, is the well pattern 5.
• the column code starts with high bit 606 and ends with low bit 605 : 000011 , or column 3.
• the row code starts with high bit 608 and ends with low bit 607: 000100, or row 4.

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