Combined use of expression and CGH arrays pinpoints novel candidate genes in Ewing sarcoma family of tumors

Abstract

BackgroundEwing sarcoma family of tumors (ESFT), characterized by t(11;22)(q24;q12), is one of the most common tumors of bone in children and young adults. In addition to EWS/FLI1 gene fusion, copy number changes are known to be significant for the underlying neoplastic development of ESFT and for patient outcome. Our genome-wide high-resolution analysis aspired to pinpoint genomic regions of highest interest and possible target genes in these areas.MethodsArray comparative genomic hybridization (CGH) and expression arrays were used to screen for copy number alterations and expression changes in ESFT patient samples. A total of 31 ESFT samples were analyzed by aCGH and in 16 patients DNA and RNA level data, created by expression arrays, was integrated. Time of the follow-up of these patients was 5–192 months. Clinical outcome was statistically evaluated by Kaplan-Meier/Logrank methods and RT-PCR was applied on 42 patient samples to study the gene of the highest interest.ResultsCopy number changes were detected in 87% of the cases. The most recurrent copy number changes were gains at 1q, 2, 8, and 12, and losses at 9p and 16q. Cumulative event free survival (ESFT) and overall survival (OS) were significantly better (P < 0.05) for primary tumors with three or less copy number changes than for tumors with higher number of copy number aberrations. In three samples copy number imbalances were detected in chromosomes 11 and 22 affecting the FLI1 and EWSR1 loci, suggesting that an unbalanced t(11;22) and subsequent duplication of the derivative chromosome harboring fusion gene is a common event in ESFT. Further, amplifications on chromosomes 20 and 22 seen in one patient sample suggest a novel translocation type between EWSR1 and an unidentified fusion partner at 20q. In total 20 novel ESFT associated putative oncogenes and tumor suppressor genes were found in the integration analysis of array CGH and expression data. Quantitative RT-PCR to study the expression levels of the most interesting gene, HDGF, confirmed that its expression was higher than in control samples. However, no association between HDGF expression and patient survival was observed.ConclusionWe conclude that array CGH and integration analysis proved to be effective methods to identify chromosome regions and novel target genes involved in the tumorigenesis of ESFT.

1q gain and CDT2 overexpression underlie an aggressive and highly proliferative form of Ewing sarcoma

“…Moreover, there is a substantial disagreement about which particular CNAs are clinically relevant in ES (Kullendorff et al, 1999;Tarkkanen et al, 1999;Brisset et al, 2001;Ozaki et al, 2001;Hattinger et al, 2002), probably because of the small size of the sample series analyzed (Knuutila et al, 1998;Kullendorff et al, 1999;Tarkkanen et al, 1999;Ferreira et al, 2008;Savola et al, 2009) and/or the use of techniques with low resolution/sensitivity (Knuutila et al, 1998;Kullendorff et al, 1999;Tarkkanen et al, 1999;Brisset et al, 2001;Ozaki et al, 2001;Hattinger et al, 2002), as most previous reports relied on karyotyping and/or metaphase CGH.…”

“…Likewise, while major efforts in the copy number alteration (CNA) profiling of ES have succeeded in assessing the frequency of recurrent genomic alterations (Knuutila et al, 1998;Kullendorff et al, 1999;Tarkkanen et al, 1999;Brisset et al, 2001;Ozaki et al, 2001;Hattinger et al, 2002;Roberts et al, 2008), few have integrated genomic and transcriptomic profiles and gained in-depth information about their correlation with clinical parameters (Ferreira et al, 2008;Savola et al, 2009). Moreover, there is a substantial disagreement about which particular CNAs are clinically relevant in ES (Kullendorff et al, 1999;Tarkkanen et al, 1999;Brisset et al, 2001;Ozaki et al, 2001;Hattinger et al, 2002), probably because of the small size of the sample series analyzed (Knuutila et al, 1998;Kullendorff et al, 1999;Tarkkanen et al, 1999;Ferreira et al, 2008;Savola et al, 2009) and/or the use of techniques with low resolution/sensitivity (Knuutila et al, 1998;Kullendorff et al, 1999;Tarkkanen et al, 1999;Brisset et al, 2001;Ozaki et al, 2001;Hattinger et al, 2002), as most previous reports relied on karyotyping and/or metaphase CGH.…”

Prognostic Role of Hepatoma-derived Growth Factor in Solid Tumors of Eastern Asia: a Systematic Review and Meta-Analysis

“…Of these articles, 60 were excluded based on the titles and abstracts because of obvious lack of relevance, and 89 were excluded because of obvious duplicated publications. The following articles were also excluded: three duplicated publications (Zhou et al, 2007b;Zhou et al, 2010a;Yang et al, 2014); three without data for HR and 95%CI calculations and adequate contact with the investigators could not be established (Natrajan et al, 2006;Mao et al, 2008;Hanada et al, 2013); two with a sample size<50 (Hsu et al, 2012;Tao et al, 2014); two in which HDGF expression was not detected by IHC methods (Savola et al, 2009;Zhang et al, 2010); three uncorrelated. Finally, 26 cohort studies were found eligible for the meta-analysis (Hu et al, 2003;Ren et al, 2004;Iwasaki et al, 2005;Uyama et al, 2006;Yamamoto et al, 2006;Yoshida et al, 2006;Chang et al, 2007;Yamamoto et al, 2007;Zhou et al, 2007a;Hu et al, 2009;Zhou et al, 2010b;Liu et al, 2011;Wang et al, 2011;Zhang et al, 2011;Chen et al, 2012a;Chen et al, 2012b;Lin et al, 2012;Han et al, 2013;Li et al, 2013a;Li et al, 2013b;Li et al, 2013c;Yang et al, 2013;Guo et al, 2014b;Song et al, 2014;Wang et al, 2014;Zhang et al, 2014), contai...…”

“…In recent years, elevated levels of hepatoma-derived growth factor (HDGF) have been observed in a variety of malignancies and high levels of HDGF appears to be associated with increased malignancy across cancers, as witnessed by the correlation with adverse characteristics such as poor patient survival (Hu et al, 2003;Ren et al, 2004;Iwasaki et al, 2005;Uyama et al, 2006;Yamamoto et al, 2006;Yoshida et al, 2006;Chang et al, 2007;Yamamoto et al, 2007;Zhou et al, 2007a;Hu et al, 2009;Savola et al, 2009;Zhang et al, 2010;Zhou et al, 2010b;Liu et al, 2011;Wang et al, 2011;Ye et al, 2011;Zhang et al, 2011;Chen et al, 2012a;Chen et al, 2012b;Hsu et al, 2012;Lin et al, 2012;Han et al, 2013;Hanada et al, 2013;Li et al, 2013a;Li et al, 2013b;Li et al, 2013c;Yang et al, 2013;Guo et al, 2014b;Song et al, 2014;Wang et al, 2014;Yang et al, 2014;Zhang et al, 2014). As a multifunctional protein Bao et al, 2014) widely expressed by many types of human cells, HDGF is involved in the regulations of a myriad of cancer cell activities during cancer transformation (Yang et al, 2013), apoptosis , angiogenesis (Ren et al, 2009), and metastasis (Chen et al, 2012a).…”

The advancements of genomics and data integration in sarcoma research

“…In sarcoma research, Man et al have reported the first application of array-based comparative genomic hybrid ization (aCGH) in osteosarcoma, which identified distinct amplifications and deletions that represent potential therapeutic targets [15] . Similarly, using aCGH and expression arrays, Savola et al have identified important copy number aberrations (CNAs) in Ewing sarcoma and correlated the number of CNAs in the tumor to patient's survival [16] . The study has detected copy number changes in 87% of the cases, and the most recurrent CNAs are gains at chromosome 1q 2, 8, and 12, and losses at 9p and 16q.…”