scholarly journals Gene Expression Profiling and Real-Time PCR Analyses Identify Novel Potential Cancer-Testis Antigens in Multiple Myeloma

2009 ◽  
Vol 183 (2) ◽  
pp. 832-840 ◽  
Author(s):  
Maud Condomines ◽  
Dirk Hose ◽  
Thierry Rème ◽  
Guilhem Requirand ◽  
Michael Hundemer ◽  
...  
Keyword(s):  
Gene Expression ◽  
Multiple Myeloma ◽  
Gene Expression Profiling ◽  
Real Time ◽  
Real Time Pcr ◽  
Expression Profiling ◽  
Cancer Testis Antigens ◽  
Potential Cancer ◽  
Cancer Testis

Cancer/Testis Genes in Multiple Myeloma: Expression Patterns and Vaccination Strategies Determined by Microarray Analysis.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 3401-3401
Author(s):  
Maud Condomines ◽  
Dirk Hose ◽  
Thierry Reme ◽  
Michael Hundemer ◽  
John De Vos ◽  
...  
Keyword(s):  
Gene Expression ◽  
Multiple Myeloma ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Tumor Escape ◽  
Event Free Survival ◽  
Chromosome X ◽  
Free Survival ◽  
Ct Antigens ◽  
Cancer Testis

Abstract Cancer-testis (CT) antigens are expressed in testis and malignant tumors, but rarely in non-gametogenic tissues. Due to this pattern, they represent attractive targets for cancer vaccination approaches. The aims of the present study were (1) to assess for the first time the expression of CT genes on a pangenomic basis in multiple myeloma (MM), (2) to provide selection strategies of CT antigens for clinical vaccination trials and (3) to assess the impact of CT gene expression on event-free survival. We report here the expression pattern of CT genes in purified MM cells (MMC) of 64 patients with newly-diagnosed MM, 12 patients with monoclonal gammopathy of unknown significance (MGUS), in normal plasma cell and B cell samples and in 20 MMC lines, using gene expression profiling (GEP). Out of 46 CT genes interrogated by the Affymetrix HG U133 Set arrays, 35 were expressed in MMC of at least one patient, according to the Affymetrix “present” call (frequency range: 2% – 66%). Of these, 24 CT genes were expressed in more than 5% of the MMC samples and 25 are located on chromosome X. MMC of 98% of the patients expressed at least one CT gene, 86% at least two, and 70% at least three CT genes. By using a set of 10 CT genes including KM-HN-1, MAGE-C1, MAGE-A3/6/12, MAGE-A5, MORC, DDX43, SPACA3, SSX-4, GAGE-1–8 and MAGE-C2, a combination of at least three CT genes - desirable to circumvent tumor escape mechanisms and immune tolerance - could be obtained in MMC of 67% of the patients. Thus, gene expression profiling can be used to select CT antigens as vaccination targets in individual patients. In a series of MMC from 111 patients treated with the same high-dose chemotherapy and autologous peripheral blood stem cell transplantation protocol and having a median two-year follow-up, we found that the expression of six CT genes, i.e. CTAG-1B, CTAG-2, MAGE-A1, MAGE-A2, MAGE-A3 and MAGE-A6 was associated with a shorter event-free survival (EFS). Furthermore, considering only the 25 CT genes encoded by chromosome X, a CT-Xhigh cluster comprising MMC of one third of the patients (35 of 111) could be defined using a binary hierarchical clustering based on Affymetrix call. Patients in the CT-Xhigh cluster had a shorter EFS (median 13 months) compared to patients in the CT-Xlow cluster (median 18 months, P = .003). The CT-Xhigh clsuter included more patients with a stage III disease (P = .004). These results confirm data from previous studies indicating that patients expressing some CT genes located on chromosome X have a poor outcome.

Identification of reference genes for quantitative real-time PCR in the bovine mammary gland during the lactation cycle

2007 ◽  
Vol 29 (3) ◽  
pp. 312-319 ◽  
Author(s):  
Massimo Bionaz ◽  
Juan J. Loor
Keyword(s):  
Gene Expression ◽  
Mammary Gland ◽  
Network Analysis ◽  
Gene Expression Profiling ◽  
Real Time ◽  
Real Time Pcr ◽  
Expression Profiling ◽  
Physiological State ◽  
Pairwise Comparison ◽  
Internal Controls

Achieving greater understanding of the genomic influence on milk synthesis in dairy cows represents a daunting challenge. Bovine-specific microarrays have allowed for high-throughput gene expression analysis of the mammary transcriptome. However, real-time PCR (qPCR) still represents the method of choice for accurate expression profiling of small numbers of genes and verification of key microarray relationships. This method is extremely sensitive but requires data normalization to account for analytical errors. Ideally, expression of genes used as internal controls should not be affected by specific treatments or physiological state. Mammary biopsies were collected from five cows each at −15, 1, 15, 30, 60, 120, and 240 days relative to parturition for gene expression profiling. We evaluated expression of nine genes ( RPS9, ACTB, GAPD, GTP, ITGB4BP, MRPL39, RPS23, RPS15, and UXT) that could serve as internal controls in mammary tissue using qPCR. Due to gradual increases in mammary RNA concentration (μg/mg tissue) over lactation, all genes investigated experienced a dilution effect. We used pairwise comparison of expression ratios to analyze the reliability of these genes as internal controls. UXT, RPS9, and RPS15 had the most stable expression ratios across cow and time. We also assessed co-regulation among genes through network analysis. Network analysis suggested co-regulation among most of the genes examined, with MYC playing a central role. Pairwise comparison was suitable for finding appropriate internal controls in mammary gland tissue. Results showed that the geometrical average of UXT, RPS9, and RPS15 expression could be used as internal control for longitudinal mammary gene expression profiling.

scholarly journals Clinical Outcome, Molecular and Gene Expression Analysis of 20 MLL-Rearranged AML from a Single Institution

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 4943-4943
Author(s):  
Sergio Burillo-Sanz ◽  
Rosario Morales-Camacho ◽  
MT Vargas ◽  
Javier Sánchez ◽  
Jose Raul Garcia-Lozano ◽  
...  
Keyword(s):  
Gene Expression ◽  
Overall Survival ◽  
Clinical Outcome ◽  
Gene Expression Profiling ◽  
Real Time ◽  
Real Time Pcr ◽  
Expression Profiling ◽  
Conflicts Of Interest ◽  
Mll Gene ◽  
Or Gene

Abstract Background Rearrangements of the mixed lineage leukemia (MLL) gene at 11q23 (due to translocation, partial tandem duplication or gene amplification) are frequent in AML. Translocations give rise to fusion genes with AF9, AF6, MLLT10 and ENL, among others; partial tandem duplications or self-fusion fuses the 5' region of an MLL into the other MLL gene; and MLL amplification results in several copies of the wild-type gene. In this work we report the molecular analysis, gene expression profiling and clinical outcome for a cohort of MLL- rearrangedAML. Patients and Methods Herein we include 20 MLL-rearrangement harboring patients, diagnosed in our institution of AML. MLL gene fusion was detected by cytogenetics; FISH with LSI MLL dual color, Break Apart probe, and chromosome painting probes; 10 cases could be verified by reverse transcription PCR (RT-PCR) and sequencing. Gene expression was analyzed in ten cases by real-time PCR in a reaction with specific primers and SybrGreen. Relative quantification was performed by 2-DDCt method. Survival analysis was carried-out by Kaplan-Meyer method. Overall survival was considered as the time from diagnostics to exitus. Results In a time course from March 2004 to June 2015, the systematic screening for genetic rearrangements in AML patients at diagnosis, revealed 20 patients harboring a rearranged MLL. Fourteen of these were translocations, and in nine of them we could demonstrate the genetic fusion at the mRNA sequence level. There were three amplifications of the MLL gene in double minute (dmin), homogeneously stained region (hsr) and in several marker chromosomes. MLL rearrangement harboring patients had a median overall survival of 284±119 (N=18) days and only 25% of them survive at 1.7 years. Gene expression profiling of AML relevant genes (HOXA5, FLT3, EVI1, MEIS1 and RUNX1) showed a general upregulation of HOXA5, and a heterogenic regulation of FLT3. EVI1 and MEIS1 expression, undetectable in health control's peripheral blood, were upregulated only in some cases, interestingly the only two survivors in the series had undetectable EVI1 expression (Fig 1A). RUNX1 had a downregulation in MLL amplification cases, especially patient with 15-20 MLL copies in HSR in hyperdiploid cells that showed 7.4*107±2.5*107 fold downregulation (p<0.01), almost undetectable by real-time PCR (Fig 1B). Also was significatively (p<0.05) downregulated in two of the four MLL-ENL harboring patients and the only included MLL-AF6 harboring patient. Conclusions In this work we show that MLL-rearranged AML have a poor outcome, and most of them should not be included in intermediate-risk karyotype. Accordingly, the classification of MLL cases by the genetic partner or gene expression profile may provide a more precise prognostics. In this sense, overexpression of EVI1 has been previously associated to a worst outcome, but there are other genes that could be useful in prognostics such as MEIS1. Figure 1. Figure 1. Disclosures No relevant conflicts of interest to declare.

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