Verification of targeted gene expression profiling panel for identifying biomarker signatures for immunotherapy research.

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. e23208-e23208
Author(s):  
Aleksandr Pankov ◽  
Yuan-Chieh Ku ◽  
Warren Tom ◽  
Jianping Zheng ◽  
Yongming Sun ◽  
...  
Keyword(s):  
Gene Expression ◽  
Immune Response ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Therapeutic Potential ◽  
Tumor Infiltrating Lymphocytes ◽  
Diagnostic Procedures ◽  
Susceptible Population ◽  
Targeted Gene Expression ◽  
Average Gene

e23208 Background: Immunotherapy has led to an unprecedented and long-lasting response in susceptible populations. Despite the therapeutic potential of the treatment, identifying biomarkers and stratifying populations that are likely to respond has been a challenge. While gene expression profiling has previously been successfully used to stratify individuals, there exist limitations with the prevalent technologies. In particular, full transcriptome gene expression estimates use limited biological material to measure the concentrations of thousands of uninformative genes and often lacks the depth required to accurately measure expression of lowly-expressed genes. These low-expressing genes may be critical to the identification of a signature associated with susceptible population. Methods: To efficiently measure the expression of the genes potentially informative of an immunotherapy response, we developed a high-throughput targeted gene expression solution measured with our RNA Ion Oncomine™ Immune Response Research Assay panel* containing 395 genes. This panel provides information about the expression of genes involved in tumor checkpoint inhibition, as well as markers of T cell signaling pathway, interferon signaling, tumor infiltrating lymphocytes (TIL). Results: We used publicly-available TCGA data to characterize the complexities of estimating unbiased gene expression from a targeted panel and developed a solution using a new normalization procedure that allows for accurate comparisons of samples within cancer types. Furthermore, we verified that lowering the RNA input amount or changing the assay operator does not contribute to a large variation in the gene expression estimates; each only accounts for less than 10% of variance of the average gene when the assay is compared across biological samples. Conclusions: Creating a panel that achieved high reproducibility and accurate expression estimates of key immune response genes allowed us to accurately separate high and low TIL samples within squamous and adenocarcinoma samples, emphasizing the utility of the panel to biomarker immunotherapy research. *For Research Use Only. Not for use in diagnostic procedures.

Targeted gene expression profiling of inverted papilloma and squamous cell carcinoma

2021 ◽  
Author(s):  
Charles C. L. Tong ◽  
Mateusz Koptyra ◽  
Pichai Raman ◽  
Komal S. Rathi ◽  
Namrata Choudhari ◽  
...  
Keyword(s):  
Gene Expression ◽  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Gene Expression Profiling ◽  
Squamous Cell ◽  
Expression Profiling ◽  
Inverted Papilloma ◽  
Targeted Gene Expression

scholarly journals Multiplexed, Targeted Gene Expression Profiling and Genetic Analysis on Electronic Microarrays

2002 ◽  
Vol 48 (11) ◽  
pp. 1873-1882 ◽  
Author(s):  
Elaine M Weidenhammer ◽  
Brenda F Kahl ◽  
Ling Wang ◽  
Larry Wang ◽  
Melanie Duhon ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Target Genes ◽  
Mrna Targets ◽  
Amplification Method ◽  
Polymorphism Detection ◽  
Targeted Gene Expression ◽  
Electronic Microarray ◽  
Electronic Field

Abstract Background: Electronic microarrays comprise independent microelectrode test sites that can be electronically biased positive or negative, or left neutral, to move and concentrate charged molecules such as DNA and RNA to one or more test sites. We developed a protocol for multiplexed gene expression profiling of mRNA targets that uses electronic field-facilitated hybridization on electronic microarrays. Methods: A multiplexed, T7 RNA polymerase-mediated amplification method was used for expression profiling of target mRNAs from total cellular RNA; targets were detected by hybridization to sequence-specific capture oligonucleotides on electronic microarrays. Activation of individual test sites on the electronic microarray was used to target hybridization to designated subsets of sites and allow comparisons of target concentrations in different samples. We used multiplexed amplification and electronic field-facilitated hybridization to analyze expression of a model set of 10 target genes in the U937 cell line during lipopolysaccharide-mediated differentiation. Performance of multiple genetic analyses (single-nucleotide polymorphism detection, gene expression profiling, and splicing isoform detection) on a single electronic microarray was demonstrated using the ApoE and ApoER2 genes as a model system. Results: Targets were detected after a 2-min hybridization reaction. With noncomplementary capture probes, no signal was detectable. Twofold changes in target concentration were detectable throughout the (∼64-fold) range of concentrations tested. Levels of 10 targets were analyzed side by side across seven time points. By confining electronic activation to subsets of test sites, polymorphism detection, expression profiling, and splicing isoform analysis were performed on a single electronic microarray. Conclusions: Microelectronic array technology provides specific target detection and quantification with advantages over currently available methodologies for targeted gene expression profiling and combinatorial genomics testing.

scholarly journals Targetable subsets of non-Hodgkin lymphoma in Malawi define therapeutic opportunities

2016 ◽  
Vol 1 (1) ◽  
pp. 84-92 ◽  
Author(s):  
Elizabeth A. Morgan ◽  
M. Patrick Sweeney ◽  
Tamiwe Tomoka ◽  
Nadja Kopp ◽  
Daniel Gusenleitner ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Hodgkin Lymphoma ◽  
Expression Profiling ◽  
Resource Constraints ◽  
Objective Assessment ◽  
Non Hodgkin Lymphoma ◽  
Key Points ◽  
Targeted Gene Expression

Key Points NHL subclassification is lacking in Malawi due to resource constraints yet is critical for directing therapy. Targeted gene expression profiling facilitates objective assessment and segregation of biologically defined subsets of NHL from Malawi.

Gene Expression Profiling within the Context of JAK Inhibitor Therapy for Myelofibrosis: Correlation with Treatment Effect and Anemia Response

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 1751-1751
Author(s):  
Animesh Pardanani ◽  
Rebecca R. Laborde ◽  
Terra L Lasho ◽  
Christy Finke ◽  
Alexey A. Leontovich ◽  
...  
Keyword(s):  
Gene Expression ◽  
Clinical Trial ◽  
Immune Response ◽  
Gene Expression Profiling ◽  
Pathway Analysis ◽  
Treatment Effect ◽  
Expression Profiling ◽  
Phase 1 ◽  
Hemoglobin Level ◽  
Jak Inhibitors

Abstract Abstract 1751 Background: JAK inhibitors have significant palliative benefit in myelofibrosis (MF), mainly in the form of improved constitutional symptoms and reduced splenomegaly. Preliminary data suggests that CYT387, a JAK-1/2 inhibitor, also has the ability to produce anemia responses (ASH Annual Meeting, 2011). In general, the mechanism(s) underlying treatment effects of JAK inhibitors remain unclear but likely represent a drug-specific balance between anti-clonal activity and modulation of immuno cellular-cytokine pathways. We conducted a gene expression profiling (GEP) study using primary cells from MF patients undergoing therapy with CYT387 followed by correlation with clinical data. Methods: Study subjects were enrolled in the Phase-1/2 study of CYT387 treatment in patients with primary (PMF), post-polycythemia vera (PPMF) or post-essential thrombocythemia (PTMF) myelofibrosis. Paired research samples were collected; the time points were pre-study and 12 weeks after commencing study treatment. PBMCs were purified from whole blood by Ficoll separation; RNA was isolated from this cell fraction for GEP analysis. Gene expression profiles were generated using Illumnia Human HT-12 v4 microarray. Pair wise analysis was conducted using the Wilcoxon signed-rank test with a p-value cutoff of 0.05 to generate lists of differentially expressed genes between assigned groups. Pathway analysis was conducted to identify relevant pathways enriched for differentially expressed genes. Comprehensive plasma cytokine profiling was performed using Multiplex Bead-Based Luminex technology (Invitrogen, Carlsbad, CA). Results: Seventeen patients were studied based on sample availability; 11 (65%) mere male with median age of 66 years (range 53–85). Twelve (71%) were JAK2V617F mutation positive and the DIPSS-plus risk categorization was 10 (59%) high and 7 (41%) intermediate-2. All patients were evaluable for anemia response; 14 (82%) were red cell transfusion dependent at study start. Nine (53%) patients achieved anemia response by IWG-MRT criteria; of these, 8 patients achieved transfusion independence (minimum non-transfused hemoglobin level of 8 g/dL maintained for at least 12 weeks) and 1 had a sustained >2 g/dL increase in hemoglobin level above baseline. The initial pair wise analysis to identify differential patterns of gene expression compared pre- and post-treatment groups (Figure 1A). This revealed a cluster of significantly (p <0.05) down-regulated genes (minimum 2-fold; median 17-fold) following treatment (displayed in green; upper left quadrant). Pathway enrichment analysis revealed significant associations of these genes with cytokine regulation of immune response, cell proliferation, chemotaxis and cytoskeleton remodeling. We then conducted a pair wise analysis of anemia responders versus non-responders; this revealed a predominance of over expressed gene targets (median 35-fold) in the anemia responder group (Figure 1B) (displayed in red; upper right quadrant). Similar pathway analysis identified enrichment for genes involved in immune system function in this cluster. Conclusions: The current preliminary analysis suggests that genes relevant to immune response-cytokine pathways are significantly over expressed in patients who achieve anemia response following CYT387 therapy. This further suggests a dominant immune component that underpins ineffective hematopoiesis in responding patients. On the basis of broad treatment-related changes in gene expression we suggest that an important component of CYT387's treatment effect is down regulation of these dysregulated pathways. Ongoing studies include validation of select gene targets which will be tested prospectively in future treatment protocols, as well as correlation of gene expression with circulating cytokine-chemokine levels. Disclosures: Pardanani: Bristol-Myers Squibb: Clinical trial support, Clinical trial support Other; YM BioSciences: Clinical trial support, Clinical trial support Other; Sanofi-Aventis: Clinical trial support Other. Off Label Use: Data from Phase −1/2 study of CYT387 use in myelofibrosis is mentioned.

scholarly journals Molecular Classification of MYC-Driven B-Cell Lymphomas by Targeted Gene Expression Profiling of Fixed Biopsy Specimens

2015 ◽  
Vol 17 (1) ◽  
pp. 19-30 ◽  
Author(s):  
Christopher D. Carey ◽  
Daniel Gusenleitner ◽  
Bjoern Chapuy ◽  
Alexandra E. Kovach ◽  
Michael J. Kluk ◽  
...  
Keyword(s):  
Gene Expression ◽  
B Cell ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Molecular Classification ◽  
B Cell Lymphomas ◽  
Biopsy Specimens ◽  
Targeted Gene Expression

scholarly journals MP87-03 TARGETED GENE EXPRESSION PROFILING WITHIN CIRCULATING TUMOR CELLS IN MCRPC

2018 ◽  
Vol 199 (4S) ◽  
Author(s):  
Udit Singhal ◽  
Yugang Wang ◽  
Zachary Reichert ◽  
Scott Tomlins ◽  
Todd Morgan
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Tumor Cells ◽  
Circulating Tumor Cells ◽  
Expression Profiling ◽  
Targeted Gene Expression
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