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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

2007-05-09 | GSE6887 | GEO

Peripheral blood lymphocytes: ALS patients vs. healthy controls

Project description:Transcripional profiling of lymphocytes from patients with amyotrophic lateral sclerosis (ALS) (n=11) and healthy control subjects (n=11). The goal was to determine disease response expression signatures relevant of ALS pathogenesis that affect brain and spinal cord. The reference design was used: each Cy5-labeled cRNA sample from ALS patient or healthy control subject was cohybridized on Agilent-014850 Whole Human Genome Microarray 4x44K G4112F with the reference pool formed with equal amounts of Cy3-labeled cRNAs from each sample from the healthy control group.

2011-12-11 | GSE28253 | GEO

Peripheral blood lymphocytes: ALS patients vs. healthy controls

2011-12-11 | E-GEOD-28253 | biostudies-arrayexpress

Transcription profiling of human kidney and peripheral blood lymphocytes from kidney transplant patients

Project description: Not available

| S-DIXA-D-1031 | biostudies-other

Comparing P53 expression and genome-wide transcriptome profiling to Comet assay in lymphocytes from melanoma patients and healthy controls.

Project description:This study compared the expression of TP53 in lymphocytes from malignant melanoma (MM) patients with positive sentinel nodes to healthy controls (HCs) following exposure to various doses of UVA radiation. The Lymphocyte Genome Sensitivity (LGS) assay indicated significant differences in DNA damage in lymphocytes between MM patients and HCs. qPCR data demonstrated an overall 3.4-fold increase in TP53 expression in lymphocytes from MM patients compared to healthy controls, following treatment with 0.5 mW/cm2 UVA radiation. Western blotting confirmed that p53 expression was increased in MM lymphocytes following UVA exposure compared to healthy individuals. Genome transcriptome profiling data displayed differences in gene expression between UVA-treated lymphocytes from MM patients and HCs. Peripheral lymphocytes from MM patients are more susceptible to the genotoxic effects of UVA compared to healthy individuals. Our previous studies showed that UVA exposure of various intensities caused significant differences in the levels of DNA damage between lymphocytes from cancer patients compared to HCs through the LGS assay. The present study's results provide further credibility to the LGS assay as a screening test for cancer detection. Peripheral lymphocytes could be a promising blood biopsy biomarker for staging of carcinomas and prevention of carcinoma progression at early stages.

| S-EPMC10620420 | biostudies-literature

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.

| S-EPMC7446107 | biostudies-literature

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

2012-03-21 | GSE32280 | GEO

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.

2012-03-21 | E-GEOD-32280 | biostudies-arrayexpress

Peripheral blood B lymphocytes derived from patients with idiopathic pulmonary arterial hypertension express a different RNA pattern compared with healthy controls: a cross sectional study.

Project description:BackgroundIdiopathic pulmonary arterial hypertension (IPAH) is a progressive and still incurable disease. Research of IPAH-pathogenesis is complicated by the lack of a direct access to the involved tissue, the human pulmonary vasculature. Various auto-antibodies have been described in the blood of patients with IPAH. The purpose of the present work was therefore to comparatively analyze peripheral blood B lymphocyte RNA expression characteristics in IPAH and healthy controls.MethodsPatients were diagnosed having IPAH according to WHO (mean pulmonary arterial pressure > or = 25 mmHg, pulmonary capillary occlusion pressure < or = 15 mmHg, absence of another explaining disease). Peripheral blood B-lymphocytes of patients and controls were immediately separated by density gradient centrifugation and magnetic beads for CD19. RNA was thereafter extracted and analyzed by the use of a high sensitivity gene chip (Affymetrix HG-U133-Plus2) able to analyze 47000 transcripts and variants of human genes. The array data were analyzed by two different softwares, and up-and down-regulations were defined as at least 1.3 fold with standard deviations smaller than fold-changes.ResultsHighly purified B-cells of 5 patients with IPAH (mean pulmonary artery pressure 51 +/- 13 mmHg) and 5 controls were analyzed. Using the two different analyzing methods we found 225 respectively 128 transcripts which were up-regulated (1.3-30.7 fold) in IPAH compared with healthy controls. Combining both methods, there were 33 overlapping up-regulated transcripts and no down-regulated B-cell transcripts.ConclusionPatients with IPAH have a distinct RNA expression profile of their peripheral blood B-lymphocytes compared to healthy controls with some clearly up-regulated genes. Our finding suggests that in IPAH patients B cells are activated.

| S-EPMC2262076 | biostudies-literature

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