title: Analysis of T-cell receptor V beta gene repertoires after immune stimulation and in malignancy by use of padlock probes and microarrays.
abstract: BACKGROUND
  Detection of expanded T-cell clones, identified by their receptor (TCR) repertoires, can assist diagnosis and guide therapy in infectious, inflammatory, and autoimmune conditions as well as in tumor immunotherapy. Analysis of tumor-infiltrating lymphocytes often reveals preferential use of one or a few TCR V beta genes, compared with peripheral blood, indicative of a clonal response against tumor antigens.
  
  
  METHODS
  To simultaneously measure the relative expression of all V beta gene families, we combined highly specific and sensitive oligonucleotide reagents, called padlock probes, with a microarray read-out format. T-Cell cDNA was combined with a pool of V beta subfamily-specific padlock probes. Reacted probes were selectively amplified and the products hybridized to a microarray, from which the V beta subfamily distribution in each sample could be determined relative to a control sample.
  
  
  RESULTS
  In lymphocytes stimulated with the superantigen staphylococcal enterotoxin B, we detected expansions at the mRNA level of TCR subfamilies previously shown to respond to staphylococcal enterotoxin B. Expansions of the same V beta families could also be detected by flow cytometry. In samples from two bladder cancer patients, we detected predominant representations of specific V beta subfamilies in both tumor-infiltrating lymphocytes and in the draining lymph nodes, but not in non-tumor-draining lymph nodes or peripheral blood. Several expression profiles from draining lymph nodes in patients with malignant melanoma were divergent from profiles seen in non-tumor-draining lymph nodes.
  
  
  CONCLUSIONS
  Padlock probe-based parallel analysis of TCR V beta gene distributions provides an efficient method for screening multiple samples for T-cell clonal expansions with reduced labor and time of analysis compared with traditional methods.
authors.affiliation: Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala Universitet, Uppsala, Sweden.
authors.forename: Johan
authors.initials: J
authors.lastname: Banér
authors.forename: Per
authors.initials: P
authors.lastname: Marits
authors.forename: Mats
authors.initials: M
authors.lastname: Nilsson
authors.forename: Ola
authors.initials: O
authors.lastname: Winqvist
authors.forename: Ulf
authors.initials: U
authors.lastname: Landegren
mesh_terms: D000230:Adenocarcinoma / Q000175:diagnosis / Q000235:genetics / Q000276:immunology; D002294:Carcinoma, Squamous Cell / Q000175:diagnosis / Q000235:genetics / Q000276:immunology; D018076:DNA, Complementary / Q000032:analysis; D004768:Enterotoxins / Q000276:immunology; D020869:Gene Expression Profiling; D019672:Genes, T-Cell Receptor; D006801:Humans; D008213:Lymphocyte Activation; D008214:Lymphocytes / Q000378:metabolism; D008545:Melanoma / Q000175:diagnosis* / Q000235:genetics / Q000276:immunology; D020411:Oligonucleotide Array Sequence Analysis; D015345:Oligonucleotide Probes; D016133:Polymerase Chain Reaction; D016693:Receptors, Antigen, T-Cell, alpha-beta / Q000096:biosynthesis / Q000235:genetics*; D012015:Reference Standards; D013211:Staphylococcus aureus / Q000276:immunology; D018089:Superantigens / Q000276:immunology; D001749:Urinary Bladder Neoplasms / Q000175:diagnosis* / Q000235:genetics / Q000276:immunology
chemical_list: D018076:DNA, Complementary; D004768:Enterotoxins; D015345:Oligonucleotide Probes; D016693:Receptors, Antigen, T-Cell, alpha-beta; D018089:Superantigens; C031818:enterotoxin B, staphylococcal