ABSTRACT
BACKGROUND: In patients with hematologic malignancies who receive stem-cell transplantation, donors' T cells can recognize minor histocompatibility antigens on recipient cells and generate an objective response against the tumor. However, a major side effect of such therapy is graft-versus-host disease (GVHD). The purpose of this study was to characterize distinct T-cell clones that were frequently and exclusively involved in GVHD or graft-versus-tumor (GVT) effects. METHODS: We hypothesized that distinct GVHD-associated T-cell clones can be identified during the disease progression. To test this, we conducted comparative analysis of T-cell receptor (TCR) Vßs in donor-recipient pairs of patients with GVHD versus those with GVHD-free and relapse-free survival using quantitative reverse-transcriptase polymerase chain reaction and spectratyping analyses. RESULTS: We identified three sets of T-cell clones that were either frequently involved in GVHD (TCR Vß4, 11, and 23) or GVT effect (TCR Vß9, 16, and 20), or were increased at the time of GVHD and GVT effects in a patient-specific manner (TCR Vß2, 3, 7, 12, 15, and 17). Spectratyping analysis showed restricted clonality of the identified TCR Vßs. Polymerase chain reaction analysis also confirmed the presence of GVHD-associated T-cell clones at the site of the disease. CONCLUSIONS: These data suggest that GVHD- and GVT-associated clones can be distinguished by molecular analysis of TCR Vß to develop targeted therapy for GVHD.
Subject(s)
Graft vs Host Disease/immunology , Receptors, Antigen, T-Cell, alpha-beta/immunology , Stem Cell Transplantation/adverse effects , T-Lymphocytes/immunology , Adult , Aged , DNA/genetics , Female , Follow-Up Studies , Gene Expression , Graft vs Host Disease/etiology , Graft vs Host Disease/pathology , Hematologic Neoplasms/surgery , Humans , Male , Middle Aged , Receptors, Antigen, T-Cell, alpha-beta/biosynthesis , Receptors, Antigen, T-Cell, alpha-beta/genetics , Reverse Transcriptase Polymerase Chain Reaction , T-Lymphocytes/pathologyABSTRACT
The 2008 ABRF DNA Sequencing Research Group (DSRG) difficult template sequencing study was designed to identify a general set of guidelines that would constitute the best approaches for sequencing difficult templates. This was a continuation of previous DSRG difficult template studies performed in 1996, 1997, and 2003. The distinguishing factors in the present study were the number of DNA templates used, the number of different types of difficult regions tested, and the inclusion of a follow-up phase of the study to identify optimal protocols for each type of difficult template. DNA templates with associated sequencing primers were distributed to participating laboratories and each laboratory returned their sequencing results along with descriptions of the experimental conditions used. The data were analyzed and the best protocols were identified for each difficult template. This information was subsequently distributed to the participating laboratories for a second round of sequencing to evaluate the general applicability of the optimized protocols. The average improvements in sequencing results were 11% overall, with a range of -25% to +43% using the optimized protocols. The full results from this study are presented here and they demonstrate that general experimental protocols and common additives can be used to improve the sequencing success for many difficult templates.
Subject(s)
DNA/chemistry , Sequence Analysis, DNA/methods , Templates, Genetic , Algorithms , Base Sequence , DNA Primers/chemistry , Evaluation Studies as Topic , Guidelines as Topic , Hot Temperature , Humans , Molecular Sequence Data , Nucleic Acid Denaturation , Software , Spectrophotometry, UltravioletABSTRACT
Over the past few years, technological advances in automated DNA sequencing have had a profound effect on the nature of DNA sequencing laboratories. To characterize the changes occurring within DNA sequencing facilities, the DNA Sequencing Research Group conducted three previous studies, in 1998, 2000, and 2003. A new general survey has been designed and conducted by the DSRG to capture the current status of DNA sequencing facilities in all sectors. Included were questions regarding facility administration, pricing, instrumentation, technology, protocols, and operation. The results of the survey are presented here, accompanied by comparisons to the previous surveys. These comparisons formed a basis for the discussion of trends within the facilities in response to the dynamics of a changing technology.
