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Transcription profiling of human peripheral blood lymphocytes: comparison between melanoma patients and healthy controls

ABSTRACT: We focused on the major peripheral blood lymphocyte populations that may be involved in anti-tumor responses and negatively impacted by cancer, specifically CD8 T cells, CD4 T cells, B cells and CD56dim natural killer cells. The pure cell subsets were stringently sorted by flow cytometry from PBMC samples. Gene expression profiles of these cell populations from melanoma patients were compared to healthy controls. Experiment Overall Design: The raw data set contained 48 arrays: 6 healthy and 6 melanoma arrays for each of the 4 cell types. Two of the arrays had quality issues due to background noise and were excluded, leaving us with 46 arrays. Experiment Overall Design: On each array we used Cy3 to label a pool of two RNA samples from a pair of age and gender matched stage IV (American Joint Committee on Cancer) melanoma patients or from a pair of age and gender matched healthy donors. We used Cy5 to label the Total Lymphocyte Reference (TLR) RNA. The TLR is a common reference specifically created for this study using the total peripheral lymphocyte fraction from 20 healthy donors.

ORGANISM(S): Homo sapiens

SUBMITTER: Critchley-Thorne RJ

PROVIDER: S-ECPF-GEOD-6887 | biostudies-other | 2007 May

REPOSITORIES: biostudies-other

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Transcription profiling of human peripheral blood lymphocytes: comparison between melanoma patients and healthy controls

Project description:We focused on the major peripheral blood lymphocyte populations that may be involved in anti-tumor responses and negatively impacted by cancer, specifically CD8 T cells, CD4 T cells, B cells and CD56dim natural killer cells. The pure cell subsets were stringently sorted by flow cytometry from PBMC samples. Gene expression profiles of these cell populations from melanoma patients were compared to healthy controls. Experiment Overall Design: The raw data set contained 48 arrays: 6 healthy and 6 melanoma arrays for each of the 4 cell types. Two of the arrays had quality issues due to background noise and were excluded, leaving us with 46 arrays. Experiment Overall Design: On each array we used Cy3 to label a pool of two RNA samples from a pair of age and gender matched stage IV (American Joint Committee on Cancer) melanoma patients or from a pair of age and gender matched healthy donors. We used Cy5 to label the Total Lymphocyte Reference (TLR) RNA. The TLR is a common reference specifically created for this study using the total peripheral lymphocyte fraction from 20 healthy donors.

2008-06-15 | E-GEOD-6887 | biostudies-arrayexpress

Gene expression profile of peripheral blood lymphocytes: comparison between melanoma patients and healthy controls

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Peripheral blood lymphocytes: ALS patients vs. healthy controls

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Prospective identification of neoantigen-specific lymphocytes in the peripheral blood of melanoma patients.

Project description:Detection of lymphocytes that target tumor-specific mutant neoantigens--derived from products encoded by mutated genes in the tumor--is mostly limited to tumor-resident lymphocytes, but whether these lymphocytes often occur in the circulation is unclear. We recently reported that intratumoral expression of the programmed cell death 1 (PD-1) receptor can guide the identification of the patient-specific repertoire of tumor-reactive CD8(+) lymphocytes that reside in the tumor. In view of these findings, we investigated whether PD-1 expression on peripheral blood lymphocytes could be used as a biomarker to detect T cells that target neoantigens. By using a high-throughput personalized screening approach, we identified neoantigen-specific lymphocytes in the peripheral blood of three of four melanoma patients. Despite their low frequency in the circulation, we found that CD8(+)PD-1(+), but not CD8(+)PD-1(-), cell populations had lymphocytes that targeted 3, 3 and 1 unique, patient-specific neoantigens, respectively. We show that neoantigen-specific T cells and gene-engineered lymphocytes expressing neoantigen-specific T cell receptors (TCRs) isolated from peripheral blood recognized autologous tumors. Notably, the tumor-antigen specificities and TCR repertoires of the circulating and tumor-infiltrating CD8(+)PD-1(+) cells appeared similar, implying that the circulating CD8(+)PD-1(+) lymphocytes could provide a window into the tumor-resident antitumor lymphocytes. Thus, expression of PD-1 identifies a diverse and patient-specific antitumor T cell response in peripheral blood, providing a novel noninvasive strategy to develop personalized therapies using neoantigen-reactive lymphocytes or TCRs to treat cancer.

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Expression data from peripheral blood lymphocytes of major depression, subsyndromal symptomatic depression, and healthy controls

Project description:Several studies have suggested that SSD is a transitory phenomena in the depression spectrum and is thus considered a subtype of depression. However, the pathophysioloy of depression remain largely obscure and studies on SSD are limited. The present study compared the expression profile and made the classification with the leukocytes by using whole-genome cRNA microarrays among drug-free first-episode subjects with SSD, MDD, and healthy controls. We used microarrays to detail the global programme of gene expression to develop blood-based gene expression profiles models for classification of subsyndromal symptomatic depression and major depressive disorder The present study compared the expression profile and made the classification with the leukocytes by using whole-genome cRNA microarrays among drug-free first-episode subjects with SSD, MDD, and matched controls (8 subjects in each group). Support vector machines (SVMs) were utilized for training and testing on candidate signature expression profiles from signature selection step.

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Project description:The IGR-Heu tumor cell line was established from patient Heu suffering from large cell carcinoma of the lung. Heu171 T cell clones were isolated from autologous tumor infiltrating lymphocytes. H32-22 clone was isolated from autologous peripheral blood lymphocytes after stimulation with IGR-Heu and sorting with peptide-MHC tetramers. T cells were grown in the presence of irradiated autologous tumor and lymphoblastoid cell lines in complete media supplemented with rIL-2 and conditioned medium from phytohemagglutinin-activated lymphocytes for 3 weeks. Then, for microarray assays, RNA was extracted from the different cells

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Transcription profiling of human T cell lines isolated from tumor infiltrating lymphocytes or peripheral blood lymphocytes of a patient with large cell carcinoma of the lung

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