geps oligonucleotide microarrays u133a & u133b  (Thermo Fisher)

Journal: International Journal of Molecular Sciences

Article Title: Tumor Biology Hides Novel Therapeutic Approaches to Diffuse Large B-Cell Lymphoma: A Narrative Review

doi: 10.3390/ijms252111384

Figure Lengend Snippet: Genetic and metabolic heterogeneity of DLBCL.

Article Snippet: , Monti et al., 2005. [ ] , , OxPhos , cluster signatures: NADH dehydrogenase complex, COX complex, ATP synthase (mitochondrial), ATP binding protein, ATP binding cassette subfamily, ATPase H+ transporter, TIMM, BFL-1/A1, MIHC, TNFA1P8, FAS, apoptosis-related protein 3, proteasome subunits, PTEN, etc. , , , , , three unsupervised clustering algorithms were used and compared: hierarchical clustering, self-organizing maps & model-based probabilistic clustering , GEPs by oligonucleotide microarrays (Affymetrix U133A & U133B) containing probe sets from 33,000 genes, FISH, morphologic analysis of TILs, IHC , DLBCL specimen from 176 patients , increased incidence of t(14;18) in OxPhos tumors; BCR/proliferation cluster had more abundant expression of cell-cycle regulatory genes, increased expression of DNA repair genes and p53, higher levels of many components of the BCR signaling cascade (CD19, Ig, CD79a, BLK, SYK, PLCγ2, MAP4K), additional B-cell–specific or essential TFs; the HR cluster was extensively studied: increased expression of T/NK cell receptor and activation pathway components, complement cascade members, macrophage/DC markers & inflammatory mediators; shared features of histologically defined T-cell/histiocyte-rich B-cell lymphoma, including fewer genetic abnormalities.

Techniques: Expressing, Microarray, Translocation Assay, Amplification, Selection, RNA Sequencing Assay, Activity Assay, DNA Sequencing, Mutagenesis, Activation Assay, Sequencing, Functional Assay, Binding Assay

Journal: Blood Advances

Article Title: Gene expression signature that predicts early molecular response failure in chronic-phase CML patients on frontline imatinib

doi: 10.1182/bloodadvances.2019000195

Figure Lengend Snippet: Distinct gene expression profile and enrichment of stem cells signature identified in diagnostic MNCs from patients who failed to achieve EMR. (A) The workflow of our study with regard to the discovery process, including samples from patients with EMR failure (n = 13) vs EMR achievement (n = 83), as defined by BCR-ABL1 percentage at 3 months. (B) Volcano plot demonstrating the effect of log2 fold change (FC) on the x-axis vs −log10 P value on the y-axis. Red circles indicate significant genes (FDR P < .05 and log2 FC > 0.6) with increased gene expression in the EMR failure patient group. Green circles indicate significant genes (FDR P < .05 and log2 FC < −0.6) with decreased gene expression in the EMR failure patient group. (C) Heatmap demonstrating the distinct gene expression patterns based on all significant probes (n = 502; FDR P < .05 and log2 FC > |0.6|). Orange represents increased gene expression level, and blue represents decreased gene expression level. The heatmap was generated using the pheatmap package. (D) GSEA indicates enrichment of stem cell signaling, cell cycle, and immune response/T lymphocytes in the EMR failure patient samples (BCR-ABL1 >10% IS at 3 months) compared with the EMR achievement patient samples (BCR-ABL1 ≤10% IS at 3 months). Blue bars represent cell cycle–related data sets. Red bars represent stem cell–related data sets. Green bars represent immune response/T lymphocyte–related signatures. Regarding normalized enrichment score (NES), positive score indicates positive enrichment in samples from patients who failed to achieve EMR, and negative score indicates enrichment in samples from patients who achieved EMR. (E) Boxplot displaying the differential blast percentage counts at diagnosis, indicating a significantly higher percentage in the samples collected from patients who failed to achieve EMR. Only 91 patients had differential blast percentage counts at diagnosis information available for analysis. (F) Boxplot displaying the lymphocyte percentage counts at diagnosis, indicating a significantly lower percentage in the EMR failure patient sample group. Only 94 patients had lymphocyte percentage counts at diagnosis information available for analysis. Statistical analysis was performed using the Mann-Whitney U test.

Article Snippet: 27 , 28 GEP microarray analysis Genome-wide GEP was performed using the Illumina Human HT-12v4 platform (containing 47 323 probes) at the Australian Genome Research Facility (Melbourne, VIC, Australia).

Techniques: Gene Expression, Diagnostic Assay, Generated, Biomarker Discovery, MANN-WHITNEY