Journal: BMC Bioinformatics

Article Title: Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: comparison of gene expression profiling approaches

doi: 10.1186/s12859-020-3365-5

Figure Lengend Snippet: Comparison of traditional and new microarray platforms with sequencing approaches

Article Snippet: Building upon large scale clinical studies to investigate the effects of endocrine therapy on breast cancer using Affymetrix U133A arrays [ ] and Illumina HT12-V4 BeadChips [ ], this study, utilised patient-matched sets of samples across a range of transcriptomic technologies: Affymetrix Clariom S, NanoString, Ion AmpliSeq Transcriptome, BioSpyder TempO-seq [ ] Lexogen QuantSeq and RNA-seq (Table ).

Techniques: Microarray, Sequencing, RNA Sequencing Assay, Amplification, Ligation, Multiplex Assay, Polymerase Chain Reaction, Hybridization, Chromatin Immunoprecipitation, Genome Wide

Journal: Cell metabolism

Article Title: Increased Tumor Glycolysis Characterizes Immune Resistance to Adoptive T cell Therapy

doi: 10.1016/j.cmet.2018.02.024

Figure Lengend Snippet: A. The linear regression of mRNA expression of ALDOA in patient-derived melanoma cell lines correlated with the percentage of T cell-mediated tumor killing is shown. Patient-derived melanoma cell lines (n=12) overexpressing Gp100 and H-2Db, which can be recognized by Pmel T cells derived from the TCR transgenic Pmel-1 mouse, were generated by lentivirus-based genetic manipulations. Transduced melanoma cells were co-cultured with Pmel T cells at an effector to target ratio of 10:1 for 3 hours. The percentage of T cell-induced tumor killing was then calculated by quantifying the number of cleaved caspase-3+ cells with respect to the total number of tumor cells by flow cytometry. The mRNA expression of glycolysis-related genes in patient-derived melanoma cells was determined by microarray analysis. The R and P-value of the correlation between the ALDOA expression and the sensitivity to T cell killing in this set of patient-derived melanoma cell lines are listed. B. Overexpression of ALDOA in melanoma cells promotes resistance to T cell-mediated tumor cell apoptosis. Patient-derived melanoma cells (Mel2400) were transduced with lentiviral vectors encoding either ALDOA-RFP or GFP-RFP. The percentage of cleaved caspase-3+ transduced melanoma cells (based on the expression of the reporter gene RFP) was determined by flow cytometry. C. The impaired effector function of TILs by lactic acid is shown. TILs (TIL2559) derived from a melanoma patient were treated overnight with different concentrations of lactic acid. *P<0.05 (with versus without lactic acid treatment) D. LDHAi increases T cell-induced killing of melanoma cells. Patient-derived melanoma cells (Mel2792) were pre-treated with 1 uM of GSK2837808A, and followed by co-culture with autologous TILs (TIL2792) for 4 hours. E. Targeting glycolysis pathway enhances the antitumor activity of T cells. B16 melanoma cells were implanted subcutaneously in C57BL/6 mice. Tumor-bearing mice were treated with either GSK2837808A (6 mg/kg) orally and/or adoptively transferred Pmel T cells. Mice treated with the relevant solvent were used as control. Tumor sizes were monitored by measuring the perpendicular diameters of the tumors and are shown as mean tumor area ± SEM. All experiments were carried out in a blinded, randomized fashion (n=4–5 mice per group). F. Kaplan-Maier plots show survivals of tumor-bearing mice treated with vehicle, GSK2837808A, T cell therapy and combination of GSK2837808A and T cell therapy (n=4–5 mice per group). *P<0.05, **P<0.01, and ****P<0.0001.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit Anti-Active Caspase-3 BD Bioscience Cat#560626; RRID:AB_1727414 Biological Samples Human Melanoma Tissues Obtained from patients enrolled in the clinical Trial (2004-0069, {"type":"clinical-trial","attrs":{"text":"NCT00338377","term_id":"NCT00338377"}} NCT00338377 ) N/A Human Melanoma Cell Lines and TILs Derived from patients enrolled in the clinical Trial (2004-0069, {"type":"clinical-trial","attrs":{"text":"NCT00338377","term_id":"NCT00338377"}} NCT00338377 ) N/A Chemicals, Peptides, and Recombinant Proteins Lactic Acid Sigma-Aldrich L1750 GSK2837808A TOCRIS 5189 Proleukin PROMETHEUS NDC 65483-116-07 Critical Commercial Assays XF Glycolysis Stress Test Kit Agilent 103020-100 XF Cell Mito Stress Test Kit Agilent 103015-100 XF Mito Fuel Flex Test Kit Agilent 103260-100 Human Cytokine/Chemokine Panel 1 EMD Millipore HCYTMAG-60K-PX41 Human Cytokine/Chemokine Panel 2 EMD Millipore HCYP2MAG-62K-PX23 Human Cytokine/Chemokine Panel 3 EMD Millipore HCYP3MAG-63K-11 HUMAN HT-12 v4 BEADCHIP Kit Illumina BD-103-0204 Deposited Data Raw and analyzed data This paper GEO: {"type":"entrez-geo","attrs":{"text":"GSE101644","term_id":"101644"}} GSE101644 Experimental Models: Cell Lines Murine B16 Melanoma Cells ATCC ATCC CRL-6475; RRID:CVCL_0159 Human A375 Melanoma Cells ATCC ATCC CRL-1619; RRID:CVCL_0132 Experimental Models: Organisms/Strains Mouse: C57BL/6Ncr Mice Charles River (Frederick Research Model Facility) Strain Code 556 Recombinant DNA pCDH-CMV-IRES-RFP System Biosciences CD500 cDNA human ALDOA DNASU Plasmid Repository HsCD00022119 Software and Algorithms Ingenuity Pathway Analysis Qiagen Bioinformatics https://www.qiagenbioinformatics.com/ Wave 2.3.0 Agilent http://www.agilent.com/ R V3.2 R project https://www.r-project.org/ Prism v6.0 Graphpad https://www.graphpad.com/ Tableau 10.1 Tableau https://www.tableau.com/ SAS 9.1 SAS Institute https://www.sas.com/en_us/home.html Other Resources related to TCGA dataset analysis TCGA https://portal.gdc.cancer.gov/ Resources related to PROSPECT dataset analysis Parra et al., 2016 N/A Open in a separate window KEY RESOURCE TABLE

Techniques: Expressing, Derivative Assay, Transgenic Assay, Generated, Cell Culture, Flow Cytometry, Microarray, Over Expression, Transduction, Co-Culture Assay, Activity Assay