Inducing, Collecting, and Storing Ascites.

Ascitic fluid (also called ascites) is an intraperitoneal fluid extracted from mice that have developed a peritoneal tumor. For antibody production, the tumor is induced by injecting hybridoma cells into the peritoneum, which serves as a growth chamber for the cells. The hybridoma cells grow to high densities and continue to secrete the antibody of interest, thus creating a high-titered solution of antibodies for collection. A single mouse may yield as much as 10 mL of ascitic fluid or as little as 1 mL per batch. Antibody concentrations will typically be between 1 and 10 mg/mL. The most common problem encountered in storing ascites is contamination of these solutions with bacteria or fungi. This can be prevented by the addition of sodium azide.

Growing Hybridomas.

This introduction discusses the techniques used to grow and maintain myeloma and hybridoma cell lines, the production and collection of monoclonal antibodies, and methods for drug selection used in hybridoma work.

Monitoring PD-1 Phosphorylation to Evaluate PD-1 Signaling during Antitumor Immune Responses.

PD-1 expression marks activated T cells susceptible to PD-1-mediated inhibition but not whether a PD-1-mediated signal is being delivered. Molecular predictors of response to PD-1 immune checkpoint blockade (ICB) are needed. We describe a monoclonal antibody (mAb) that detects PD-1 signaling through the detection of phosphorylation of the immunotyrosine switch motif (ITSM) in the intracellular tail of mouse and human PD-1 (phospho-PD-1). We showed PD-1+ tumor-infiltrating lymphocytes (TILs) in MC38 murine tumors had high phosphorylated PD-1, particularly in PD-1+TIM-3+ TILs. Upon PD-1 blockade, PD-1 phosphorylation was decreased in CD8+ TILs. Phospho-PD-1 increased in T cells from healthy human donors after PD-1 engagement and decreased in patients with Hodgkin lymphoma following ICB. These data demonstrate that phosphorylation of the ITSM motif of PD-1 marks dysfunctional T cells that may be rescued with PD-1 blockade. Detection of phospho-PD-1 in TILs is a potential biomarker for PD-1 immunotherapy responses.

Selecting for and Checking Cells with HGPRT Deficiency for Hybridoma Production.

For drug-selective media to work for hybridoma selection, myeloma cells expressing a mutation abrogating the function of their HGPRT gene (and subsequently unable to produce purines for DNA biosynthesis) are used. HGPRT will recognize 8-AG as a substrate and convert it to the monophosphate nucleotide. The 8-AG-containing nucleotide is then processed further and incorporated into DNA and RNA, where it is toxic. Therefore, cells with a functional HGPRT enzyme grown in the presence of 8-AG will die. Cells that are deficient in HGPRTase cannot incorporate 8-AG in vivo and thus continue to grow. Cells that have been selected for resistance to 8-AG should be checked periodically to ensure that they maintain sensitivity to drugs that block the de novo synthesis of DNA. In addition, all myeloma cell lines should be checked periodically for reversion of their drug selection markers. Any line that is not killed completely by drug selection should either be reselected or replaced with a new line.

Preparing mFc- and hFc-Fusion Proteins from Mammalian Cells.

Fc-fusion proteins are composed of an immunoglobulin Fc domain that is directly linked to the antigen of interest. Typically, these vectors will contain an amino-terminal signal sequence that permits trafficking to the cell surface and secretion into the media and a carboxy-terminal Fc receptor that enables purification on Protein A-Sepharose. Fc-fusion proteins have several applications in protein microarrays, oncological therapies, and vaccine and antibody development. Presence of the Fc domain significantly increases the plasma life of the fusion partner, which prolongs therapeutic activity. Furthermore, the Fc domain enhances the solubility and stability of the partner molecule. Because Fc-fusion proteins are secreted into the culture medium, purification by affinity chromatography is relatively easy and cost-effective. Immunizing a murine host with mFc-fusion protein generates an antigen-specific immune response because the Fc domain is recognized as "self" by the host.

Testing Hybridoma Cells for Mycoplasma Contamination.

Because mycoplasmas are a diverse group of organisms and are difficult to culture, several different strategies for detecting mycoplasma contamination have been developed. To date, no one test is suitable for detecting all of the possible mycoplasmas that may contaminate hybridoma or myeloma cultures. Therefore, it is sensible to consider using several methods. The most commonly used techniques are described here. Mycoplasma screening by growth on microbial medium can be performed on agar plates or in broth culture. Cultures are grown under both aerobic and anaerobic conditions because some common strains of Mycoplasma prefer the lack of oxygen (Mycoplasma buccale, Mycoplasma faucium, M. orale, and M. salivarium). Mycoplasma colonies form a characteristic "fried egg" appearance on agar plates, and this is the diagnostic feature used to confirm mycoplasma contamination. The colonies are small and are most easily seen with an inverted microscope. A quicker method for testing for mycoplasma takes advantage of the DNA-intercalating dye Hoechst 33258. Fixed cells are stained with the dye, and contaminated cultures are detected by the bright, punctate cytoplasmic staining of the Mycoplasma DNA. Finally, commercial kits for the detection of mycoplasmas using colorimetric assays or reporter cells are also described.

Ridding Hybridoma Cells of Mycoplasma Contamination.

Resistance to the most common antibiotics is what makes elimination of mycoplasma contamination so difficult, but not impossible. Different species of Mycoplasma have varied sensitivities to each of the major classes of antibiotics. One method presented here entails selection in antibiotic-containing medium combined with single-cell cloning over activated macrophage feeders. Its success rate is as high as 70%. As a method of last resort, growing hybridoma cells as ascites tumors is one of the most effective methods of removing mycoplasma contamination. The mycoplasmas are removed from the hybridoma cell surface by the immune system of the mouse. Mice must be of the same genetic background as the hybridomas. This technique is the same as the method for ridding cells of bacterial or fungal infection, and the success rate is perhaps 80%.

Liquid Nitrogen Storage of Hybridoma Cells.

Hybridoma and myeloma cell lines can be stored by slowly freezing cells in an appropriate solution of nutrients and a cryoprotectant such as glycerol or dimethyl sulfoxide (DMSO). In this protocol, cells are centrifuged at 4°C, resuspended in cold freezing solution (10% DMSO in FBS), and then transferred to an appropriate freezing vial. The vials are slowly frozen to -70°C in Styrofoam racks and then stored in liquid nitrogen (LN2). Cells stored in LN2 will remain viable for years. Once a frozen vial has been removed from LN2 storage, it should be thawed as described, grown out into log phase, and refrozen.

Subtractive Immunization for Mice, Rats, and Hamsters.

Subtractive immunization is useful for directing the immune response away from dominant epitopes to allow antibodies against less immunogenic antigens to be developed. It is also useful when there is a need to downplay the response to carriers added to peptides and recombinant proteins, such as Gst and Ig, to aid in production and purification. Subtractive immunization protocols also can be helpful if the target protein is part of a mixture (such as a cell lysate) or present on the surface of transfected cells.

Detecting Protein Antigens in Sodium Dodecyl Sulfate-Polyacrylamide Gels.

In some cases, a native protein can be isolated in its pure form from cell lysates or tissue preparation using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Antigens purified this way often induce good antibody responses. After electrophoresis, the band of protein of interest must be located in the gel. A variety of identification methods can be used, all of which are designed to avoid excessive fixation of the protein in the gel matrix. The choice of method depends partly on the abundance of the polypeptide. Three methods are commonly used: (1) staining side strips cut from the edge of the gel, (2) light staining of the gel itself, and (3) locating the band by radioactive labeling of the antigen. Staining strips of the gel cut from its sides avoids the need to fix the gel. When isolating abundant proteins that are well separated from other bands, staining side strips is a useful method. If the protein is not abundant or is located close to a contaminating band making a clean excision difficult, use one of the other staining methods. If the protein is reasonably abundant, then a light staining of the proteins in the gel with Coomassie Blue G will permit localization without fixing. Alternatively, the bands in the gel can be visualized by immersing the gel in sodium acetate or copper chloride. If the protein is radiolabeled with 125I, 32P, or 35S, then use an autoradiogram as a template to excise the band of interest.

Preparing Feeder Cell Cultures to Support Hybridoma Growth.

Feeder layer plates are prepared with cells that provide the appropriate growth factors to support the growth of hybridoma cells until they can expand in number and provide their own. Good feeder cells should have properties that allow them to be selected against during the future growth of the hybridomas. Peritoneal macrophages, myeloma cells, splenocytes, and MRC-5 cells (a human lung fibroblast line) are the most common feeder layer cells used in hybridoma fusions. Methods for their preparation are described here.

Single-Cell Cloning of Hybridoma Cells by Growth in Soft Agar.

Single-cell cloning during hybridoma production ensures that cells that produce the antibody of interest are truly monoclonal and that the secretion of this antibody can be stably maintained. Cloning of hybridoma cells in semisolid medium is one of the most commonly used methods for producing single-cell clones. The technique is easy, but, because it is performed in two stages, it does take longer than other methods. Not all cells will grow in soft agar, and there may be a bias on the type of colony that appears. However, most of the commonly used myeloma fusion partners have relatively good cloning efficiencies in soft agar, and, consequently, so do most hybridomas. Even though every attempt is made to ensure that the cells are in a single-cell suspension before plating, there is no way to guarantee that the colonies do not arise from two cells that were stuck together. Therefore, single-cell cloning in soft agar should be repeated at least twice before the cells are considered clonal.

Electro Cell Fusion for Hybridoma Production.

Once a good immune response has developed in an animal and an appropriate screening procedure has been developed, the construction of hybridomas is ready to begin. The electro cell fusion (electrofusion) method uses an electrical field in the form of short, intense pulses to increase the permeability of the membrane. The resulting local perforation of the cell membrane induces the cells to fuse, forming hybridomas. Electrofusion is accomplished in three steps: Prealignment of the cells (convergence and cell contact), membrane fusion, and postalignment (rounding off the fused cells). This method has been applied successfully to hybridoma production with higher efficiency than routine polyethylene glycol fusion, allowing production of more hybrid cells.

Myeloma and Hybridoma Cell Counts and Viability Checks.

For most purposes, the number of hybridoma or myeloma cells can be estimated simply by observing the cells under the microscope. When an exact cell count is needed, the number can be determined by using a hemocytometer (improved Neubauer counting chambers are the most commonly used). This is a simple device in which a special coverslip rests on supports that hold it 0.1 mm above the base of the slide. The slide is engraved with a series of lines that form 1 × 1-mm squares. By counting the number of cells within the 0.1-mm3 chamber formed by the 1 × 1-mm square and the height of the coverslip, an accurate quantitation of cells per milliliter can be calculated. To determine the percentage of viable cells within a population, the cell suspension is mixed with a vital dye and observed under the microscope. Vital dyes are excluded from living cells but stain dead cells. The most common dye used for these stains is Trypan Blue.

Making Weak Antigens Strong: Cross-Linking Peptides to KLH with Maleimide.

Haptens, which are small antigens such as peptides and drug compounds, are very weakly or nonimmunogenic by themselves and require the assistance of carrier proteins: complex molecules capable of eliciting a strong immune response in the host on injection. The haptens serve as epitopes for binding to the antibodies on the B-cell surface, and the carriers provide the MHC class II-T-cell receptor binding sites. Keyhole limpet hemocyanin (KLH) is one of the most widely used of such carrier proteins. KLH-hapten conjugates are commonly used in antibody generation in a variety of hosts such as mice, rats, and rabbits. Because KLH is harvested from mollusks, it is physiologically distant from mammalian species and less likely to produce antibodies that cross-react mammalian antigens. Maleimide activation of carrier proteins makes it possible to conjugate sulfhydryl-containing haptens, and hence this chemistry is widely used for conjugating KLH with haptens.

Screening for Good Batches of Fetal Bovine Serum for Myeloma and Hybridoma Growth.

Not all lots of fetal bovine serum (FBS) are good at supporting hybridoma growth at low density. The key constituents that distinguish good batches of serum from bad are not known. It is necessary to order test batches from several suppliers and screen them as described here or purchase prescreened serum directly from the distributor.

Polyethylene Glycol Fusion for Hybridoma Production.

Once a good immune response has developed in an animal and an appropriate screening procedure has been developed, the construction of hybridomas is ready to begin. Polyethylene glycol (PEG) is the fusing agent of choice for hybridoma production, allowing the rapid and manageable fusion of mammalian cells. PEG fuses the plasma membranes of adjacent myeloma and/or antibody-secreting cells, forming a single cell with two or more nuclei. This heterokaryon retains these nuclei until the nuclear membranes dissolve before mitosis. In this protocol, antibody-secreting cells are isolated from the appropriate lymphoid tissue (mouse spleen and lymph nodes), mixed with myeloma cells, centrifuged to generate good cell-to-cell contacts, and fused with PEG. The fused cells are then diluted into selective medium and plated in multiwell tissue culture dishes. Beginning ∼1 wk later, samples of the tissue culture supernatants are removed from wells that contain growing hybridomas and tested for the presence of the appropriate antibodies. Cells from positive wells are grown, single-cell-cloned, and frozen. A procedure for screening batches of PEG for efficacy before hybridoma fusion is also included.

PD-L1 Antibodies to Its Cytoplasmic Domain Most Clearly Delineate Cell Membranes in Immunohistochemical Staining of Tumor Cells.

Blocking the programmed death-1 (PD-1) pathway has clinical benefit in metastatic cancer and has led to the approval of the mAbs pembrolizumab and nivolumab to treat melanoma and nivolumab for non-small cell lung cancer. Expression of PD-L1 on the cell surface of either tumor cells or infiltrating immune cells is associated with a higher likelihood of response to PD-1 blockade in multiple studies. Most mAbs to PD-L1 in use are directed to its extracellular domain and immunohistochemically stain tumor tissue with a mixture of cytoplasmic and membrane staining. Cytoplasmic staining obscures the interpretation of a positive reaction on the tumor cell membrane, and thus affects the accuracy of PD-L1 scoring systems. We developed a mAb to the cytoplasmic domain of PD-L1, 405.9A11 (9A11), which is both more selective for membranous PD-L1 and more sensitive in IHC and Western blotting, compared with previous mAbs specific for the PD-L1 extracellular domain. Here, we compare immunohistochemical staining patterns of PD-L1 expression in five types of tumors, using five PD-L1 mAbs: 9A11, 7G11, and three commercially available mAbs. We demonstrate that 9A11, as well as two other cytoplasmic domain-specific mAbs, E1L3N and SP142, can clearly delineate the membrane of PD-L1-positive cells in formalin-fixed paraffin-embedded tissue and facilitate interpretation of staining results.

Cross-reactivity of the BRAF VE1 antibody with epitopes in axonemal dyneins leads to staining of cilia.

Antibodies that recognize neo-epitopes in tumor cells are valuable tools in the evaluation of tissue biopsy or resection specimens. The VE1 antibody that recognizes the V600E-mutant BRAF protein is one such example. We have recently shown that the vast majority of papillary craniopharyngiomas-tumors that arise in the sellar or suprasellar regions of the brain-harbor BRAF V600E mutations. The VE1 antibody can be effective in discriminating papillary craniopharyngioma from adamantinomatous craniopharyngioma, which harbors mutations in CTNNB1 and not BRAF. While further characterizing the use of the VE1 antibody in the differential diagnosis of suprasellar lesions, we found that the VE1 antibody stains the epithelial cells lining Rathke's cleft cysts with very strong staining of the cilia of these cells. We used targeted sequencing to show that Rathke's cleft cysts do not harbor the BRAF V600E mutation. Moreover, we found that the VE1 antibody reacts strongly with cilia in various structures-the bronchial airways, the fallopian tubes, the nasopharynx, and the epididymis-as well as with the flagella of sperm. In addition, VE1 reacts strongly with the cilia of the ependymal lining of the brain and with the cilia-containing microlumens of ependymoma tumors. There is significant sequence homology between the synthetic peptide (amino acid 596-606 of BRAF V600E: GLATEKSRWSG) that was used to generate the VE1 antibody and regions of multiple axonemal dynein heavy chain proteins (eg, DNAH2, DNAH7, and DNAH12). These proteins are major components of the axonemes of cilia and flagella where they drive the sliding of microtubules. In ELISA assays, we show that the VE1 antibody recognizes epitopes from these proteins. A familiarity with the cross-reactivity of the VE1 antibody with epitopes of proteins in cilia is of value when evaluating tissues stained with this important clinical antibody.

Bat3 promotes T cell responses and autoimmunity by repressing Tim-3­mediated cell death and exhaustion.

T cell immunoglobulin and mucin domain­containing 3 (Tim-3) is an inhibitory receptor that is expressed on exhausted T cells during infection with HIV-1 and hepatitis C virus. By contrast, Tim-3 expression and function are defective in multiple human autoimmune diseases. However, the molecular mechanisms modulating Tim-3 function are not well understood. Here we show that human leukocyte antigen B (HLA-B)-associated transcript 3 (Bat3) binds to, and represses the function of, Tim-3. Bat3 protects T helper type 1 (TH1) cells from galectin-9­mediated cell death and promotes both proliferation and proinflammatory cytokine production. Bat3-deficient T cells have elevated expression of exhaustion-associated molecules such as Tim-3, Lag3, Prdm1 and Pbx3, and Bat3 knockdown in myelin-antigen­specific CD4+ T cells markedly inhibits the development of experimental autoimmune encephalomyelitis while promoting the expansion of a dysfunctional Tim-3hi, interferon-γ (IFN-γ)loCD4+ cell population. Furthermore, expression of Bat3 is reduced in exhausted Tim-3+ T cells from mouse tumors and HIV-1­infected individuals. These data indicate that Bat3 acts as an inhibitor of Tim-3­dependent exhaustion and cell death. Bat3 may thus represent a viable therapeutic target in autoimmune disorders, chronic infections and cancers.