Current studies have on the identification of novel antigens expressed in melanoma and renal cancers as well as the characterization of T cells that recognize epitopes of previously described antigens. In a series of recent studies, several novel point-mutated genes have been identified as the targets of melanoma-reactive TIL that mediated long terms clinical tumor regression following adoptive transfer. Current investigations are being carried out to develop methods to facilitate the identification of mutated gene products that can be evaluated as targets of tumor-reactive T cells. Recent studies have focused on the use of high throughput sequencing to identify all of the somatic mutations in patient tumors. Minigenes encoding the somatic mutations identified from tumor sequencing have been generated and tested for their ability to be recognized by autologous TIL. Screening of individual tumor infiltrating lymphocyte (TIL) generated from tumor fragments for their ability to recognize candidate mutated antigens or neoantigens has resulted in the identification of one or more mutated antigen targets in 80-90% of patients with melanoma, gastrointestinal, breast, lung and ovarian cancers. In recent studies carried out in a patient with cholangiocarcinoma, analysis of reactivity with a mutated antigen was used to guide the selection of TIL used for treatment of a patient who has demonstrated significant regression of multiple metastatic lesions. Partial tumor regressions have also been observed in a patient with colon cancer treated with autologous TIL that predominantly recognized a hotspot mutation in the KRAS oncogene and a breast cancer patient whose TIL recognized two neoantigens. Ongoing efforts are focused on the optimizing strategies for identifying neoantigen reactive T cells, including studies involving the use of MHC binding algorithms to identify minimal T cell epitopes and studies comparing multiple screening approaches for their sensitivity and specificity. For these studies, the DNA Core facility provides multiple services members of the Surgery Branch that include construction and analysis of whole exome sequencing (WES) and RNA-seq expression libraries, RT-PCR, quantitative RT-PCR, gene cloning and RNA/DNA analysis. In carrying out bioinformatics analysis of WES and RNA-seq data, the DNA Core provides investigators with lists of candidate neoantigens for screening with patient T cells, along with valuable information regarding tumor cell chromosomal copy number variations and data regarding hotspot driver mutations, and evaluate tumor samples for expression of genes involved with tumor antigen processing and presentation. The FACS Core Facility is currently being utilized for the analysis of T cell populations that are administered to patients as a part of the analysis of ongoing clinical cancer adoptive immunotherapy trials. In addition, the FACS Core is utilized on a daily basis for the analysis of the results of experiments to analyze the results of in vitro experiments to examine factors that influence the phenotype and function of tumor reactive T cells as well as to carry out the separation of cells based upon their expression of a wide variety of cell surface markers. For these studies phenotypic analyses are being carried out on a BD FACSCalibur, FACSCantoI, FACSCantoII, as well as a recently acquired LSRFortessa, and cell separations were carried out on a BD FACSAriaII.
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