Gene expression profiling for prediction of treatment response

2004 ◽  
Vol 22 (14_suppl) ◽  
pp. 9594-9594
Author(s):  
J. Cossman ◽  
K. Johnson ◽  
J. Gottlieb ◽  
M. Elashoff
2009 ◽  
Vol 27 (15_suppl) ◽  
pp. 574-574
Author(s):  
M. Y. Iddawela ◽  
Y. Wang ◽  
R. Russell ◽  
G. Cowley ◽  
M. El-Sheemy ◽  
...  

574 Background: FFPE is a valuable and widely available resource for translational research which to date has been under-used due to technical limitations. Improvement in technology has enabled genome-wide analysis of FFPE samples. We have assessed gene expression and copy number changes in the same cohort of breast cancers to identify markers or pathways important in prediction of treatment response. Methods: FFPE tissues from patients treated with neoadjuvant adriamycin/cyclophosphamide followed by taxanes in a clinical study were used. Gene expression profiling was assessed using the cDNA mediated annealing selection and ligation assay using the cancer panel which assess 502 genes (DASL assay, Illumina). Data was analysed using BeadStudio software. Copy number changes were assessed using the Molecular inversion probe assay with the 50K SNP panel (Affymetrix, California) and analysed using Nexus software (Biodiscovery). Results: Gene expression profiling was carried out on 44 samples. 12/44 (27%) patients had a pathological complete response (pCR) following chemotherapy. Significant differential expression of genes between pCR and non-pCR cancers were shown. TNFRSF5, CTSD, BCL3, ARNT, BIRC3, TGFBR1, MLLT6, and EVI2A were over-expressed and COL18A1, FGF12, IGFBP1 and NOTCH4 which were down-regulated in cancers that have a pCR (p ≤ 0.01). Copy number changes were assessed in 33 samples and comparison of copy number changes in pCR vs. non-pCR showed gains in regions 6q22, 21q21, 4p14, 4q21, 4p14, and loss at 11q11 (p ≤ 0.01). Three regions containing microRNA coding sequences, mir130a (11q11) mir142 (17q23) and mir21 (17q23) showed significant loss among pCR tumours (p < 0.05). Conclusions: This feasibility study shows that FFPE can be used for gene expression and copy number analysis which is a useful tool for the discovery of predictive markers for treatment response in neoadjuvant treatment trials. The role of TNFRSF5, microRNA 21/130a/142, and 11q11 loss should be further investigated as predictive markers of response to chemotherapy. [Table: see text]


2021 ◽  
Author(s):  
Monika Dmitrzak-Weglarz ◽  
Aleksandra Szczepankiewicz ◽  
Janusz Rybakowski ◽  
Paweł Kapelski ◽  
Karolina Bilska ◽  
...  

Abstract Introduction This study aimed to find the expression biomarkers of pharmacological treatment response in a naturalistic hospital setting. Through gene expression profiling, we were able to find differentially-expressed genes (DEGs) in unipolar (UD) and bipolar (BD) depressed women. Methods We performed gene expression profiling in hospitalized women with unipolar (n=24) and bipolar depression (n=32) who achieved clinical improvement after pharmacological treatment (without any restriction). To identify DEGs in peripheral blood mononuclear cells (PBMCs), we used the SurePrint G3 Microarray and GeneSpring software. Results After pharmacological treatment, UD and BD varied in the number of regulated genes and ontological pathways. Also, the pathways of neurogenesis and synaptic transmission were significantly up-regulated. Our research focused on DEGs with a minimum fold change (FC) of more than 2. For both types of depression, 2 up-regulated genes, OPRM1 and CELF4 (p=0.013), were significantly associated with treatment response (defined as a 50% reduction on the Hamilton Depression Rating Scale [HDRS]). We also uncovered the SHANK3 (p=0.001) gene that is unique for UD and found that the RASGRF1 (p=0.010) gene may be a potential specific biomarker of treatment response for BD. Conclusion Based on transcriptomic profiling, we identified potential expression biomarkers of treatment outcomes for UD and BD. We also proved that the Ras-GEF pathway associated with long-term memory, female stress response, and treatment response modulation in animal studies impacts treatment efficacy in patients with BD. Further studies focused on the outlined genes may help provide predictive markers of treatment outcomes in UD and BD.


2004 ◽  
Vol 11 (S2) ◽  
pp. S112-S112
Author(s):  
C. P. Duong ◽  
A. Kowalczyk ◽  
A. Thompson ◽  
R. Chen ◽  
J. Spillane ◽  
...  

2012 ◽  
Vol 23 ◽  
pp. v12
Author(s):  
O. Balacescu ◽  
L. Balacescu ◽  
M. Rus ◽  
R. Buiga ◽  
O. Tudoran ◽  
...  

2004 ◽  
Vol 22 (14_suppl) ◽  
pp. 9594-9594
Author(s):  
J. Cossman ◽  
K. Johnson ◽  
J. Gottlieb ◽  
M. Elashoff

2002 ◽  
Vol 69 ◽  
pp. 135-142 ◽  
Author(s):  
Elena M. Comelli ◽  
Margarida Amado ◽  
Steven R. Head ◽  
James C. Paulson

The development of microarray technology offers the unprecedented possibility of studying the expression of thousands of genes in one experiment. Its exploitation in the glycobiology field will eventually allow the parallel investigation of the expression of many glycosyltransferases, which will ultimately lead to an understanding of the regulation of glycoconjugate synthesis. While numerous gene arrays are available on the market, e.g. the Affymetrix GeneChip® arrays, glycosyltransferases are not adequately represented, which makes comprehensive surveys of their gene expression difficult. This chapter describes the main issues related to the establishment of a custom glycogenes array.


2007 ◽  
Vol 177 (4S) ◽  
pp. 93-93
Author(s):  
Toshiyuki Tsunoda ◽  
Junichi Inocuchi ◽  
Darren Tyson ◽  
Seiji Naito ◽  
David K. Ornstein

2004 ◽  
Vol 171 (4S) ◽  
pp. 198-199 ◽  
Author(s):  
Ximing J. Yang ◽  
Jun Sugimura ◽  
Maria S. Tretiakova ◽  
Bin T. Teh

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