Homozygous deletion in a neuroblastoma cell line defined by a high‐density STS map spanning human chromosome band 1p36

Chen, Ying Zhang; Soeda, Eiichi; Yang, Hong; Takita, Junko; Chai, Limin; Horii, Akira; Inazawa, Johji; Ohki, Masafumi; Hayashi, Yasuhide

doi:10.1002/gcc.1151

Cited by 20 publications

(11 citation statements)

References 34 publications

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“…The effect of DNA methylation and histone deacetylation events of 30 genes in the 1p36 chromosomal region extending from markers D1S508 and D1S244, bp 7 765 595 -11 019 814 (UCSC version, May 2004; URL: http://genome.ucsc.edu) were explored. This SRO of deletions is in agreement with SRO studies presented by other groups (Caron et al, 2001;Chen et al, 2001). Yet, other groups have presented SRO located more distal on 1p (Bauer et al, 2001;White et al, 2005).…”

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confidence: 93%

Genetic and epigenetic changes in the common 1p36 deletion in neuroblastoma tumours

et al. 2007

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Chromosome 1p is frequently deleted in neuroblastoma (NB) tumours. The commonly deleted region has been narrowed down by loss of heterozygosity studies undertaken by different groups. Based on earlier mapping data, we have focused on a region on 1p36 (chr1: 7 765 595 -11 019 814) and performed an analysis of 30 genes by exploring features such as epigenetic regulation, that is DNA methylation and histone deacetylation, mutations at the DNA level and mRNA expression. Treatment of NB cell lines with the histone deacetylase inhibitor trichostatin A led to increased gene transcription of four of the 30 genes, ERRFI1 (MIG-6), PIK3CD, RBP7 (CRBPIV) and CASZ1, indicating that these genes could be affected by epigenetic downregulation in NBs. Two patients with nonsynonymous mutations in the PIK3CD gene were detected. One patient harboured three variations in the same exon, and p.R188W. The other patient had the variation p.M655I. In addition, synonymous variations and one variation in an intronic sequence were also found. The mRNA expression of this gene is downregulated in unfavourable, compared to favourable, NBs. One nonsynonymous mutation was also identified in the ERRFI1 gene, p.N343S, and one synonymous. None of the variations above were found in healthy control individuals. In conclusion, of the 30 genes analysed, the PIK3CD gene stands out as one of the most interesting for further studies of NB development and progression.

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confidence: 93%

Genetic and epigenetic changes in the common 1p36 deletion in neuroblastoma tumours

et al. 2007

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“…This region is proximal to ours with minimal overlap, but their distal boundary is defined by only one case. Finally, two groups have identified a 1p36 homozygous deletion in the NB-1 neuroblastoma cell line (Ohira et al, 2000;Chen et al, 2001). However, this deletion is proximal to the SRD defined by us and most other groups, and it was not found in the primary tumor from which the cell line was derived.…”

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confidence: 77%

Expression and sequence analysis of candidates for the 1p36.31 tumor suppressor gene deleted in neuroblastomas

et al. 2007

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Neuroblastomas are characterized by 1p deletions, suggesting that a tumor suppressor gene (TSG) resides in this region. We have mapped the smallest region of deletion (SRD) to a 2 Mb region of 1p36.31 using microsatellite and single nucleotide polymorphisms. We have identified 23 genes in this region, and we have analysed these genes for mutations and RNA expression patterns to identify candidate TSGs. We sequenced the coding exons of these genes in 30 neuroblastoma cell lines. Although rare mutations were found in 10 of the 23 genes, none showed a pattern of genetic change consistent with homozygous inactivation. We examined the expression of these 23 genes in 20 neuroblastoma cell lines, and most showed readily detectable expression, and no correlation with 1p deletion. However, 7 genes showed uniformly low expression in the lines, and 2 genes (CHD5, RNF207) had virtually absent expression, consistent with the expected pattern for a TSG. Our mutation and expression analysis in neuroblastoma cell lines, combined with expression analysis in normal tissues, putative function and prior implication in neuroblastoma pathogenesis, suggests that the most promising TSG deleted from the 1p36 SRD is CHD5, but TNFRSF25, CAMTA1 and AJAP1 are also viable candidates.

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“…Frequent LOH on chromosome 1p36 has been implicated in the progression of intrahepatic cholangiocarcinoma, the second most common liver malignancy (11), and has also been well documented in neuroblastomas (12). Although allelic losses on 1p36 have been suggested to be associated with poor differentiated histologic grade in epithelial ovarian carcinoma (13), deletions on 1p36.12 were found in the early dysplastic lesions and cirrhotic nodules of hepatocellular carcinoma (7).…”

Section: Discussionmentioning

confidence: 99%

“…The DFFA gene mapped to 1p36.22 encodes the active subunit of the apoptotic nuclease DNA fragmentation factor (DFF45) (17). Although DFFA has been reported to be homozygously deleted in a neuroblastoma cell line, the role of DFFA in human liver carcinogenesis remains to be investigated (12). Thus far, RIZ is the only tumor suppressor gene that has been suggested in the pathogenesis of hepatocellular carcinoma (18).…”

Section: Discussionmentioning

confidence: 99%

Identification of Four Distinct Regions of Allelic Imbalances on Chromosome 1 by the Combined Comparative Genomic Hybridization and Microsatellite Analysis on Hepatocellular Carcinoma

et al. 2002

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Frequent chromosome 1 abnormalities detected in human hepatocellular carcinoma have been implicated in early genetic events of liver carcinogenesis. Recurrent loss of 1p with a common deleted region 1p36 -p34 has been reported from microsatellite analysis, whereas common gain of the whole chromosome q-arm was described from several comparative genomic hybridization studies. The relationships between copy number changes and allelic status however remains unclear. In this study, we have conducted a simultaneous comparative genomic hybridization and microsatellite analysis study on chromosome 1 in 31 hepatocellular carcinoma cases. Microsatellite analysis revealed frequent loss of heterozygosity on 1p at loci D1S468 (74%), D1S450 (67%), D1S2667 (65%), D1S2697 (75%), D1S199 (52%), and D1S234 (67%) corresponded to the distal 1p36 region and coincided with 12 cases (86%) that presented losses on 1p by comparative genomic hybridization analysis. Although comparative genomic hybridization indicated a common deleted region of 1p36 -p35 in the current series, microsatellite analysis has refined the smallest overlapping region (SOR) to 1p36.13-p36.22. Gain of 1q as revealed by comparative genomic hybridization suggested low and high-level gains, and cases that displayed an amplicon below the heterochromatic region 1q21-q25. Common allelic imbalances of polymorphic markers D1S2635 (64%), D1S484 (67%), D1S2878 (65%), D1S196 (70%), D1S249 (64%) D1S2785 (75%), D1S2842 (73%) and D1S2836 (74%) that corresponded to the regions 1q23.1-q24.2, 1q32.1 and 1q43-q44 were detected. Three distinct regions of allelic imbalances were thus suggested on recurring 1q gain found in hepatocellular carcinoma. Furthermore, microsatellite analysis has enabled a mapping of common overrepresented regions and suggested SOR on 1q23.1-q23.3 (D1S2635-D1S2878), 1q25.1-q31.1 (D1S452-D1S238), and 1q43 (D1S2785-D1S2842). Our current study has refined chromosome 1 aberrations in hepatocellular carcinoma to four regions of allelic imbalances. The SORs delineated should provide basis for further molecular investigation in hepatocarcinogenesis on genes residing on these chromosomal regions.

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Homozygous deletion in a neuroblastoma cell line defined by a high‐density STS map spanning human chromosome band 1p36

Cited by 20 publications

References 34 publications

Genetic and epigenetic changes in the common 1p36 deletion in neuroblastoma tumours

Genetic and epigenetic changes in the common 1p36 deletion in neuroblastoma tumours

Expression and sequence analysis of candidates for the 1p36.31 tumor suppressor gene deleted in neuroblastomas

Identification of Four Distinct Regions of Allelic Imbalances on Chromosome 1 by the Combined Comparative Genomic Hybridization and Microsatellite Analysis on Hepatocellular Carcinoma

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