Chromosomal and genetic imbalances in Chinese patients with rhabdomyosarcoma detected by high-resolution array comparative genomic hybridization

Rhabdomyosarcoma (RMS) is the most common soft-tissue sarcoma in children. Although associations between ARMS tumorigenesis and PAX3, PAX7, and FKHR are well recognized, the complete genetic etiology underlying RMS pathogenesis and progression remains unclear. Chromosomal copy number variations (CNVs) and the involved genes may play important roles in the pathogenesis and progression of human malignancies. Using high-resolution array comparative genomic hybridization (aCGH), we examined 20 formalin-fixed, paraffin-embedded (FFPE) RMS tumors to explore the involvement of the relevant chromosomal regions with resident genes in RMS tumorigenesis. In RMS, frequent gains were identified on chromosome regions 12q13.3-q14.1, 12q24.31, 17q25.1, 1q21.1, and 7q11.23, whereas frequent losses were observed on chromosome regions 5q13.2, 14q32.33, and 15q11.2. Amplifications were observed on chromosome regions 9p13.3, 12q13.3-q14.1, 12q15, and 16p13.11, whereas deletions were detected on chromosome regions 1p36.33, 1p13.1, 2q11.1, 5q13.2, 8p23.1, 9p24.3, and 16p11.2. Frequent gains were detected in GLI1, GEFT, OS9, and CDK4 (12q13.3-q14.1), being 60% in embryonal rhabdomyosarcoma (ERMS) and 66.67% in alveolar rhabdomyosarcoma (ARMS), respectively. However, frequent losses were detected in IGHG1, IGHM, IGHG3, and IGHG4 (14q32.33), being 70% in ERMS and 55.56% in and ARMS, respectively. Frequent gains were detected in TYROBP, HCST, LRFN3, and ALKBH6 (19q13.12) in ERMS but not in ARMS. The frequency of TYROBP, HCST, LRFN3, and ALKBH6 gains is significantly different in ERMS versus ARMS (P=0.011). The results suggest that novel TYROBP, HCST, LRFN3, and ALKBH6 genes may play important roles in ERMS. The technique used is a feasible approach for array comparative genomic hybridization analysis in archival tumor samples.     

Advantage of FISH analysis using FKHR probes for an adjunct to diagnosis of rhabdomyosarcomas

Translocations can be detected using fluorescence in situ hybridization (FISH) in formalin-fixed paraffin-embedded tissues. Recently, a commercially available FKHR (13q14) dual-color, break-apart rearrangement probe has been developed. However, the advantages of using this probe have not been reported. This study demonstrated the usefulness of this probe for the clinical diagnosis of rhabdomyosarcomas (RMS). We studied 33 RMS (19 embryonal rhabdomyosarcomas [ERMS], including three sclerosing-type RMS, and 14 alveloar rhabdomyosarcomas [ARMS]). Fluorescence signals were detected for 18 of the 19 (94.7%) ERMS and 13 of the 14 (92.8%) ARMS. A split-signal pattern was detected in 12 of 13 (92.3%) ARMS but was not detected in any of the ERMS, including the three sclerosing-type RMS. Amplification and polyploidy were present in both the ERMS and the ARMS. Our FISH study highlighted the excellent performance of the presently reported commercial break-apart probe for the detection of FKHR gene rearrangements in RMS. Because amplification and polyploidy were detected in both the ERMS and the ARMS, sufficient care should be taken when counting the nuclear signals. No rearrangements of the FKHR gene were found in any of the three sclerosing-type RMS when examined using a FISH assay, supporting the hypothesis that sclerosing RMS can be included as an ERMS.     

利用比较基因组杂交技术分析横纹肌肉瘤中染色体基因组的变化特征

目的 探讨横纹肌肉瘤(RMS)基因组DNA的变化特征.方法 在一步法RT-PCR检测所有标本PAX3/PAX7-FKHR mRNA融合基因表达情况的基础上,应用比较基因组杂交技术分析25例原发性RMS患者,其中腺泡状横纹肌肉瘤(ARMS)10例,胚胎性横纹肌肉瘤(ERMS)12例,多形性横纹肌肉瘤(PRMS)3例.根据融合基因表达情况、组织学分型、临床分期、组织学分级、性别和年龄进行分组比较.同时收集RMS细胞株A204(腺泡型)、RD(胚胎型)作为对照.结果 25例RMSCGH分析结果显示:(1)RMS中发生DNA拷贝数扩增最常见的部位是2p和12q,其他依次为6p、9q、10q、1p、2q、6q、8q、15q和18q(30%),发生DNA拷贝数丢失最常见的部位是3p、11P和6p(30%).(2)ARMS扩增最常见的染色体臂是12q、2p、6、2q、4q、10q和15q(30%),缺失最常见的染色体臂是3p、6p、1q、5q(30%);ERMS扩增最常见的染色体臂是7p、9q、2p、18q和1 p、8q(30%),缺失最常见的染色体臂是11p.基因组变化在不同的组织学分类中差异无统计学意义(P0.05).(3)伴有融合基因组扩增最常见的染色体臂是12q、2、6、10q、4q和15q(30%),缺失最常见的染色体臂是3 p、6p、5q(30%);不伴有融合基因组扩增最常见的染色体臂是2p、9q、18q(30%),基因组缺失最常见的染色体臂是11p和14q(30%).12q扩增在这两组间的差异有统计学意义(P<0.05),并多见于伴有融合基因的RMS.(4)在临床分期分组中,9q扩增在Ⅱ期和Ⅲ～Ⅳ期间差异有统计学意义(P<0.05),且多见于Ⅱ期患者.结论 (1)2p、12q、6p、9q、10q、lp、2q、6q、8q、15q、18q扩增及3p、11p、6p缺失可能与RMS发病相关;(2)12q扩增可能与融合基因相关;(3)9q扩增可能与RMS发病早期有关.     

Chromosomal imbalances in pleomorphic rhabdomyosarcomas and identification of the alveolar rhabdomyosarcoma-associated PAX3-FOXO1A fusion gene in one case

Rhabdomyosarcomas (RMS) are soft tissue sarcomas resembling developing skeletal muscle, and pleomorphic rhabdomyosarcomas (PRMS) are a rare nonpediatric entity. Little molecular cytogenetic information exists for PRMS, and their relationship to other subtypes of rhabdomyosarcoma and other sarcomas is unclear. Chromosomal imbalances were determined in seven well-characterized cases of PRMS using comparative genomic hybridization. The smallest overlapping regions of gain were 1p22 approximately p33 (71%), 7p (43%), 18/18q (43%), and 20/20p (43%), and the regions of loss were 10q23 (71%), 15q21 approximately q22 (57%), 3p, 5q32 approximately qter, and 13 (all 43%). Four of the seven cases had amplicons involving the regions 1p21 approximately p31, 1q21 approximately q25, 3p12, 3q26 approximately qtel, 4q28 approximately q31, 8q21 approximately q23/8q, and 22q. These regions are distinct from those frequently associated with the alveolar subtype, whereas the embryonal subtype without anaplasia is rarely associated with amplification events other than gain/amplification of 8q material. The regions of imbalance appeared more similar to those reported for malignant fibrous histiocytomas (MFH) and osteosarcomas, consistent with the suggestion that PRMS can be considered part of the spectrum of MFH. In addition, one of the cases classified as PRMS showed evidence for the presence of a PAX3-FOXO1A fusion gene, which is characteristic of the alveolar subtype of RMS.     

Clonal chromosome abnormalities in a plexiform cellular schwannoma

Rhabdomyosarcoma (RMS) is the most common soft-tissue sarcoma of childhood, accounting for 5%-8% of all pediatric malignancies. RMS can be categorized into several subtypes, including embryonal RMS (ERMS), the botryoid and spindle cell variants of ERMS, and alveolar RMS (ARMS). The t(2;13)(q35;q14) and the variant t(1;13)(p36;q14) are seen in a majority of ARMS cases. In contrast, the embryonal subtype of rhabdomyosarcoma has not been associated with a recurring chromosomal translocation. We describe here a novel chromosomal t(2;20)(q35;p12) occurring in a case of childhood RMS with embryonal histology. It is notable that this translocation harbors breakpoints at or near the locus of the PAX3 gene, which is involved in the most common recurring translocation associated with ARMS.     

Genetic heterogeneity in rhabdomyosarcoma revealed by SNP array analysis

Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in children and adolescents. Alveolar (ARMS) and embryonal (ERMS) histologies predominate, but rare cases are classified as spindle cell/sclerosing (SRMS). For treatment stratification, RMS is further subclassified as fusion‐positive (FP‐RMS) or fusion‐negative (FN‐RMS), depending on whether a gene fusion involving PAX3 or PAX7 is present or not. We investigated 19 cases of pediatric RMS using high resolution single‐nucleotide polymorphism (SNP) array. FP‐ARMS displayed, on average, more structural rearrangements than ERMS; the single FN‐ARMS had a genomic profile similar to ERMS. Apart from previously known amplification (e.g., MYCN, CDK4, and MIR17HG) and deletion (e.g., NF1, CDKN2A, and CDKN2B) targets, amplification of ERBB2 and homozygous loss of ASCC3 or ODZ3 were seen. Combining SNP array with cytogenetic data revealed that most cases were polyploid, with at least one case having started as a near‐haploid tumor. Further bioinformatic analysis of the SNP array data disclosed genetic heterogeneity, in the form of subclonal chromosomal imbalances, in five tumors. The outcome was worse for patients with FP‐ARMS than ERMS or FN‐ARMS (6/8 vs. 1/9 dead of disease), and the only children with ERMS showing intratumor diversity or with MYOD1 mutation‐positive SRMS also died of disease. High resolution SNP array can be useful in evaluating genomic imbalances in pediatric RMS. © 2015 Wiley Periodicals, Inc.     

Cytogenetic and molecular studies of an unusual case of multiple primary alveolar rhabdomyosarcomas: low-level chromosomal instability and reciprocal translocation t(6;11)

Cytogenetic and molecular studies have shown that approximately 80% of cases of alveolar rhabdomyosarcoma (ARMS) have consistent chromosomal translocation of either t(2;13) or t(1;13), resulting in either PAX3-FKHR or PAX7-FKHR gene fusions. However, 20% of the cases diagnosed histologically are negative for these fusion genes. The clinical and pathological properties of the so-called fusion gene negative tumors remain to be defined. We present an unusual case of a 7-year-old boy who developed three separate primary ARMS over a 5-year period, with the first tumor diagnosed at the age of 12 months. The tumors were negative for the characteristic translocations, t(2;13) or t(1;13), but showed evidence of low-level chromosomal instability and a reciprocal chromosomal translocation t(6;11)(q27;q13). PCR amplification of the p53 gene, exons 2-11, followed by DNA sequencing did not detect any germline p53 mutation. These clinical and cytogenetic features have not been reported previously in ARMS. The findings suggest that cytogenetic abnormalities of chromosome 6 may be associated with the development of early onset multiple ARMS in a subgroup of pediatric patients as seen in this case.     

Genomic and clinical analyses of 2p24 and 12q13‐q14 amplification in alveolar rhabdomyosarcoma: A report from the Children's Oncology Group

Alveolar rhabdomyosarcoma (ARMS) is an aggressive pediatric cancer that is related to the skeletal muscle lineage and characterized by recurrent chromosomal translocations. Within the ARMS category, there is clinical and genetic heterogeneity, consistent with the premise that “primary” genetic events collaborate with “secondary” events to give rise to subsets with varying clinical features. Previous studies demonstrated that genomic amplification occurs frequently in ARMS. In the current study, we used oligonucleotide arrays to localize two common amplicons to the 2p24 and 12q13‐q14 chromosomal regions. Based on the copy number array data, we sublocalized the minimum common regions of 2p24 and 12q13‐q14 amplification to a 0.83 Mb region containing the DDX1 and MYCN genes, and a 0.55 Mb region containing 27 genes, respectively. Using fluorescent in situ hybridization assays to measure copy number of the 2p24 and 12q13‐q14 regions in over 100 cases, we detected these amplicons in 13% and 12% of cases, respectively. Comparison with fusion status revealed that 2p24 amplification occurred preferentially in cases positive for PAX3‐FOXO1 or PAX7‐FOXO1 while 12q13‐q14 amplification occurred preferentially in PAX3‐FOXO1‐positive cases. Expression studies demonstrated that MYCN was usually overexpressed in cases with 2p24 amplification while multiple genes were overexpressed in cases with 12q13‐q14 amplification. Finally, although 2p24 amplification did not have a significant association with clinical outcome, 12q13‐q14 amplification was associated with significantly worse failure‐free and overall survival that was independent of gene fusion status. © 2009 Wiley‐Liss, Inc.     

Structural analysis of PAX7 rearrangements in alveolar rhabdomyosarcoma

In the pediatric cancer alveolar rhabdomyosarcoma, the common 2;13 and less frequent 1;13 translocations fuse PAX3 and PAX7, respectively, with FKHR to produce chimeric genes. To compare structural features of these rearrangements, we cloned and mapped a 64-kb genomic region containing PAX7 exons 5 through 8. With the use of Southern blot methodology, rearrangements of the 30-kb PAX7 intron 7 were detected in 9 of 9 PAX7-FKHR-positive cases. Similar to our t(2;13) studies, the t(1;13) breakpoints were randomly distributed within the seventh intron. In contrast with the > 90% frequency of reciprocal rearrangements in the t(2;13), reciprocal rearrangements involving the 3' PAX7 region were detected in only 4 of 9 cases. Furthermore, we detected PAX7-FKHR genomic amplification in 10 of 11 cases, in contrast with the < 5% frequency of PAX3-FKHR amplification. The differences in occurrence, reciprocity, and amplification between the PAX3-FKHR and PAX7-FKHR fusions indicate important differences in the mechanism of the two associated chromosomal translocation events.