oligonucleotide microarray hybridization  (Veracyte Inc)

Journal: Journal for Immunotherapy of Cancer

Article Title: Analysing the tumor transcriptome of prostate cancer to predict efficacy of Lu-PSMA therapy

doi: 10.1136/jitc-2023-007354

Figure Lengend Snippet: Association of immune marker signatures with PSA response and OS. (A) The correlations between the 24 non-redundant (ie, those without high Spearman correlations among each other) set of evaluated tumor immune microenvironment gene expression signatures (ρ is shown), (B) OS of the group with tumor immune gene expression signature analysis is not significantly different from the overall cohort of Lu-PSMA therapy treated patients at our institution and (C) the cDNA yield from RNA extracted from tumor samples, best PSA response and relative expression signature level (z-scores, higher values indicate higher signature) of immune-related gene signatures are shown correspondingly to identify patterns of signatures with regard to PSA response. Patients with higher PD-L2 signature (above the median) have longer OS time (D) and greater PSA responses (E). Lu-PSMA, [ 177 Lu]Lutetium-PSMA-617; mo., months; OS, overall survival; PD-L1, programmed death-ligand 1; PSA, prostate-specific antigen.

Article Snippet: RNA was extracted from formalin-fixed paraffin embedded tumor tissue and underwent cDNA amplification, oligonucleotide microarray hybridization and microarray quality control in a Clinical Laboratory Improvement Amendments-certified laboratory (Veracyte, San Diego, California, USA) as previously described.

Techniques: Marker, Gene Expression, Expressing

Journal: PLoS ONE

Article Title: In Vivo Identification of Solar Radiation-Responsive Gene Network: Role of the p38 Stress-Dependent Kinase

doi: 10.1371/journal.pone.0010776

Figure Lengend Snippet: (A) Simulated solar irradiation (SSR) of abdominal areas, at doses of 2 and 4 J/cm 2 , five hours before plastic surgery. Five women with a median age of 42 years, with phototype of II or III according to Fitzpatrick classification, were included in a photobiological study. (B) Microarray workflow. Non-irradiated and irradiated samples were separately compared to a reference, containing pooled samples (non-irradiated and irradiated). Significance Analysis of Microarrays (SAM) and a false discovery rate (FDR) of zero were used to identify transcripts that were differentially expressed between irradiated and non-irradiated conditions. SAM comparing 2 J/cm 2 with non-irradiated samples identified 288 differentially regulated genes; comparison between 4 J/cm 2 -irradiated and non-irradiated samples identified a set of 473 differentially regulated genes; and 3-class SAM identified a set of 476 genes .

Article Snippet: Hybridization was performed using an Agilent oligonucleotide microarray in situ Hybridization-Plus kit, following the manufacturer's instructions.

Techniques: Irradiation, Microarray

Journal: PLoS ONE

Article Title: In Vivo Identification of Solar Radiation-Responsive Gene Network: Role of the p38 Stress-Dependent Kinase

doi: 10.1371/journal.pone.0010776

Figure Lengend Snippet: Genes showing differential regulation only in response to the higher dose of SSR are annotated with several GO terms. Up-regulated genes (A) were associated with terms that included negative regulation of cellular processes, morphogenesis of anatomical structures, JAK-STAT signaling, nucleosome assembly and the immune response (inflammatory response and cell differentiation were also found for 1 MED (minimal erythema dose: 2 J/cm 2 ), as indicated in red); for down-regulated genes (B), GO terms were predominantly associated with transcription and regulation, although three GO terms (in red) relating to “regulation of transcription” were also observed for 1 MED . (C) Microarray data were validated for 11 genes (nine up and two down-regulated): mRNA was assayed by qPCR and normalized to the values for 18S mRNA. These genes were selected from the list of differentially expressed genes, for their classification as inflammatory response genes or their involvement in the p53 pathway. Error bars represent standard deviation. Stars indicate significant differences (two-tailed Student's t-test) between control and irradiated samples: * P<0.05; ** P<0.01; *** P<0.001.

Article Snippet: Hybridization was performed using an Agilent oligonucleotide microarray in situ Hybridization-Plus kit, following the manufacturer's instructions.

Techniques: Cell Differentiation, Microarray, Standard Deviation, Two Tailed Test, Irradiation