CHD5, a tumor suppressor gene deleted from 1p36.31 in neuroblastomas

Tomoyuki Fujita, Jun Igarashi, Erin R. Okawa, Takahiro Gotoh, Jayanthi Manne, Venkatadri Kolla, Jessica Signoff, Huaqing Zhao, Bruce R. Pawel, Wendy B. London, John M. Maris, Peter S. White, Garrett M. Brodeur

Research output: Contribution to journalArticle

124 Citations (Scopus)

Abstract

Background: Neuroblastomas are characterized by hemizygous 1p deletions, suggesting that a tumor suppressor gene resides in this region. We previously mapped the smallest region of consistent deletion to a 2-Mb region of 1p36.31 that encodes 23 genes. Based on mutation analysis, expression pattern, and putative function, we identified CHD5 as the best tumor suppressor gene candidate. Methods: We determined the methylation status of the CHD5 gene promoter in NLF and IMR5 (with 1p deletion) and SK-N-SH and SK-N-FI neuroblastoma cell lines using methylation-specific sequencing and measured CHD5 mRNA expression by reverse transcription polymerase chain reaction in cells treated with or without 5-aza-2-deoxycytidine, an inhibitor of DNA methylation. We transfected the cells with CHD5 and antisense (AS) CHD5 DNA to assess the effect of CHD5 overexpression and suppression, respectively, on colony formation in soft agar and growth of xenograft tumors in athymic mice. We also analyzed the association of CDH5 expression with outcomes of 99 neuroblastoma patients. Statistical tests were two-sided. Results: CHD5 expression was very low or absent in neuroblastoma cell lines. The CHD5 promoter was highly methylated in NLF and IMR5 lines, and CHD5 expression increased after treatment with 5-aza-2-deoxycytidine. Clonogenicity and tumor growth were abrogated in NLF and IMR5 cells overexpressing CHD5 compared with antisense CHD5 (clonogenicity: mean no. of colonies per plate, NLF-CHD5, 43 colonies, 95% confidence interval [CI] = 35 to 51 colonies, vs NLF-CHD5-AS, 74 colonies, 95% CI = 62 to 86 colonies, P <. 001; IMR5-CHD5, 11 colonies, 95% CI = 2 to 20 colonies, vs IMR5-CHD5-AS, 39 colonies, 95% CI = 17 to 60 colonies, P =. 01; tumor growth, n = 10 mice per group: mean tumor size at 5 weeks, NLF-CHD5, 0.36 cm3, 95% CI = 0.17 to 0.44 cm3, vs NLF-CHD5-AS, 1.65 cm3, 95% CI = 0.83 to 2.46 cm3, P =. 002; IMR5-CHD5, 0.28 cm3, 95% CI = 0.18 to 0.38 cm3, vs IMR5-CHD5-AS, 1.15 cm3, 95% CI = 0.43 to 1.87 cm3; P =. 01). High CHD5 expression was strongly associated with favorable event-free and overall survival (P <. 001), even after correction for MYCN amplification and 1p deletion (P =. 027). Conclusions: CHD5 is the strongest candidate tumor suppressor gene that is deleted from 1p36.31 in neuroblastomas, and inactivation of the second allele may occur by an epigenetic mechanism.

Original languageEnglish (US)
Pages (from-to)940-949
Number of pages10
JournalJournal of the National Cancer Institute
Volume100
Issue number13
DOIs
StatePublished - Jul 1 2008
Externally publishedYes

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Tumor Suppressor Genes
Neuroblastoma
Confidence Intervals
decitabine
Methylation
Neoplasms
Growth
Antisense DNA
Cell Line
DNA Methylation
Heterografts
Epigenomics
Nude Mice
Genes
Reverse Transcription
Disease-Free Survival
Agar
Alleles
Polymerase Chain Reaction
Messenger RNA

ASJC Scopus subject areas

  • Cancer Research
  • Oncology

Cite this

Fujita, T., Igarashi, J., Okawa, E. R., Gotoh, T., Manne, J., Kolla, V., ... Brodeur, G. M. (2008). CHD5, a tumor suppressor gene deleted from 1p36.31 in neuroblastomas. Journal of the National Cancer Institute, 100(13), 940-949. https://doi.org/10.1093/jnci/djn176

CHD5, a tumor suppressor gene deleted from 1p36.31 in neuroblastomas. / Fujita, Tomoyuki; Igarashi, Jun; Okawa, Erin R.; Gotoh, Takahiro; Manne, Jayanthi; Kolla, Venkatadri; Signoff, Jessica; Zhao, Huaqing; Pawel, Bruce R.; London, Wendy B.; Maris, John M.; White, Peter S.; Brodeur, Garrett M.

In: Journal of the National Cancer Institute, Vol. 100, No. 13, 01.07.2008, p. 940-949.

Research output: Contribution to journalArticle

Fujita, T, Igarashi, J, Okawa, ER, Gotoh, T, Manne, J, Kolla, V, Signoff, J, Zhao, H, Pawel, BR, London, WB, Maris, JM, White, PS & Brodeur, GM 2008, 'CHD5, a tumor suppressor gene deleted from 1p36.31 in neuroblastomas', Journal of the National Cancer Institute, vol. 100, no. 13, pp. 940-949. https://doi.org/10.1093/jnci/djn176
Fujita T, Igarashi J, Okawa ER, Gotoh T, Manne J, Kolla V et al. CHD5, a tumor suppressor gene deleted from 1p36.31 in neuroblastomas. Journal of the National Cancer Institute. 2008 Jul 1;100(13):940-949. https://doi.org/10.1093/jnci/djn176
Fujita, Tomoyuki ; Igarashi, Jun ; Okawa, Erin R. ; Gotoh, Takahiro ; Manne, Jayanthi ; Kolla, Venkatadri ; Signoff, Jessica ; Zhao, Huaqing ; Pawel, Bruce R. ; London, Wendy B. ; Maris, John M. ; White, Peter S. ; Brodeur, Garrett M. / CHD5, a tumor suppressor gene deleted from 1p36.31 in neuroblastomas. In: Journal of the National Cancer Institute. 2008 ; Vol. 100, No. 13. pp. 940-949.
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title = "CHD5, a tumor suppressor gene deleted from 1p36.31 in neuroblastomas",
abstract = "Background: Neuroblastomas are characterized by hemizygous 1p deletions, suggesting that a tumor suppressor gene resides in this region. We previously mapped the smallest region of consistent deletion to a 2-Mb region of 1p36.31 that encodes 23 genes. Based on mutation analysis, expression pattern, and putative function, we identified CHD5 as the best tumor suppressor gene candidate. Methods: We determined the methylation status of the CHD5 gene promoter in NLF and IMR5 (with 1p deletion) and SK-N-SH and SK-N-FI neuroblastoma cell lines using methylation-specific sequencing and measured CHD5 mRNA expression by reverse transcription polymerase chain reaction in cells treated with or without 5-aza-2-deoxycytidine, an inhibitor of DNA methylation. We transfected the cells with CHD5 and antisense (AS) CHD5 DNA to assess the effect of CHD5 overexpression and suppression, respectively, on colony formation in soft agar and growth of xenograft tumors in athymic mice. We also analyzed the association of CDH5 expression with outcomes of 99 neuroblastoma patients. Statistical tests were two-sided. Results: CHD5 expression was very low or absent in neuroblastoma cell lines. The CHD5 promoter was highly methylated in NLF and IMR5 lines, and CHD5 expression increased after treatment with 5-aza-2-deoxycytidine. Clonogenicity and tumor growth were abrogated in NLF and IMR5 cells overexpressing CHD5 compared with antisense CHD5 (clonogenicity: mean no. of colonies per plate, NLF-CHD5, 43 colonies, 95{\%} confidence interval [CI] = 35 to 51 colonies, vs NLF-CHD5-AS, 74 colonies, 95{\%} CI = 62 to 86 colonies, P <. 001; IMR5-CHD5, 11 colonies, 95{\%} CI = 2 to 20 colonies, vs IMR5-CHD5-AS, 39 colonies, 95{\%} CI = 17 to 60 colonies, P =. 01; tumor growth, n = 10 mice per group: mean tumor size at 5 weeks, NLF-CHD5, 0.36 cm3, 95{\%} CI = 0.17 to 0.44 cm3, vs NLF-CHD5-AS, 1.65 cm3, 95{\%} CI = 0.83 to 2.46 cm3, P =. 002; IMR5-CHD5, 0.28 cm3, 95{\%} CI = 0.18 to 0.38 cm3, vs IMR5-CHD5-AS, 1.15 cm3, 95{\%} CI = 0.43 to 1.87 cm3; P =. 01). High CHD5 expression was strongly associated with favorable event-free and overall survival (P <. 001), even after correction for MYCN amplification and 1p deletion (P =. 027). Conclusions: CHD5 is the strongest candidate tumor suppressor gene that is deleted from 1p36.31 in neuroblastomas, and inactivation of the second allele may occur by an epigenetic mechanism.",
author = "Tomoyuki Fujita and Jun Igarashi and Okawa, {Erin R.} and Takahiro Gotoh and Jayanthi Manne and Venkatadri Kolla and Jessica Signoff and Huaqing Zhao and Pawel, {Bruce R.} and London, {Wendy B.} and Maris, {John M.} and White, {Peter S.} and Brodeur, {Garrett M.}",
year = "2008",
month = "7",
day = "1",
doi = "10.1093/jnci/djn176",
language = "English (US)",
volume = "100",
pages = "940--949",
journal = "Journal of the National Cancer Institute",
issn = "0027-8874",
publisher = "Oxford University Press",
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}

TY - JOUR

T1 - CHD5, a tumor suppressor gene deleted from 1p36.31 in neuroblastomas

AU - Fujita, Tomoyuki

AU - Igarashi, Jun

AU - Okawa, Erin R.

AU - Gotoh, Takahiro

AU - Manne, Jayanthi

AU - Kolla, Venkatadri

AU - Signoff, Jessica

AU - Zhao, Huaqing

AU - Pawel, Bruce R.

AU - London, Wendy B.

AU - Maris, John M.

AU - White, Peter S.

AU - Brodeur, Garrett M.

PY - 2008/7/1

Y1 - 2008/7/1

N2 - Background: Neuroblastomas are characterized by hemizygous 1p deletions, suggesting that a tumor suppressor gene resides in this region. We previously mapped the smallest region of consistent deletion to a 2-Mb region of 1p36.31 that encodes 23 genes. Based on mutation analysis, expression pattern, and putative function, we identified CHD5 as the best tumor suppressor gene candidate. Methods: We determined the methylation status of the CHD5 gene promoter in NLF and IMR5 (with 1p deletion) and SK-N-SH and SK-N-FI neuroblastoma cell lines using methylation-specific sequencing and measured CHD5 mRNA expression by reverse transcription polymerase chain reaction in cells treated with or without 5-aza-2-deoxycytidine, an inhibitor of DNA methylation. We transfected the cells with CHD5 and antisense (AS) CHD5 DNA to assess the effect of CHD5 overexpression and suppression, respectively, on colony formation in soft agar and growth of xenograft tumors in athymic mice. We also analyzed the association of CDH5 expression with outcomes of 99 neuroblastoma patients. Statistical tests were two-sided. Results: CHD5 expression was very low or absent in neuroblastoma cell lines. The CHD5 promoter was highly methylated in NLF and IMR5 lines, and CHD5 expression increased after treatment with 5-aza-2-deoxycytidine. Clonogenicity and tumor growth were abrogated in NLF and IMR5 cells overexpressing CHD5 compared with antisense CHD5 (clonogenicity: mean no. of colonies per plate, NLF-CHD5, 43 colonies, 95% confidence interval [CI] = 35 to 51 colonies, vs NLF-CHD5-AS, 74 colonies, 95% CI = 62 to 86 colonies, P <. 001; IMR5-CHD5, 11 colonies, 95% CI = 2 to 20 colonies, vs IMR5-CHD5-AS, 39 colonies, 95% CI = 17 to 60 colonies, P =. 01; tumor growth, n = 10 mice per group: mean tumor size at 5 weeks, NLF-CHD5, 0.36 cm3, 95% CI = 0.17 to 0.44 cm3, vs NLF-CHD5-AS, 1.65 cm3, 95% CI = 0.83 to 2.46 cm3, P =. 002; IMR5-CHD5, 0.28 cm3, 95% CI = 0.18 to 0.38 cm3, vs IMR5-CHD5-AS, 1.15 cm3, 95% CI = 0.43 to 1.87 cm3; P =. 01). High CHD5 expression was strongly associated with favorable event-free and overall survival (P <. 001), even after correction for MYCN amplification and 1p deletion (P =. 027). Conclusions: CHD5 is the strongest candidate tumor suppressor gene that is deleted from 1p36.31 in neuroblastomas, and inactivation of the second allele may occur by an epigenetic mechanism.

AB - Background: Neuroblastomas are characterized by hemizygous 1p deletions, suggesting that a tumor suppressor gene resides in this region. We previously mapped the smallest region of consistent deletion to a 2-Mb region of 1p36.31 that encodes 23 genes. Based on mutation analysis, expression pattern, and putative function, we identified CHD5 as the best tumor suppressor gene candidate. Methods: We determined the methylation status of the CHD5 gene promoter in NLF and IMR5 (with 1p deletion) and SK-N-SH and SK-N-FI neuroblastoma cell lines using methylation-specific sequencing and measured CHD5 mRNA expression by reverse transcription polymerase chain reaction in cells treated with or without 5-aza-2-deoxycytidine, an inhibitor of DNA methylation. We transfected the cells with CHD5 and antisense (AS) CHD5 DNA to assess the effect of CHD5 overexpression and suppression, respectively, on colony formation in soft agar and growth of xenograft tumors in athymic mice. We also analyzed the association of CDH5 expression with outcomes of 99 neuroblastoma patients. Statistical tests were two-sided. Results: CHD5 expression was very low or absent in neuroblastoma cell lines. The CHD5 promoter was highly methylated in NLF and IMR5 lines, and CHD5 expression increased after treatment with 5-aza-2-deoxycytidine. Clonogenicity and tumor growth were abrogated in NLF and IMR5 cells overexpressing CHD5 compared with antisense CHD5 (clonogenicity: mean no. of colonies per plate, NLF-CHD5, 43 colonies, 95% confidence interval [CI] = 35 to 51 colonies, vs NLF-CHD5-AS, 74 colonies, 95% CI = 62 to 86 colonies, P <. 001; IMR5-CHD5, 11 colonies, 95% CI = 2 to 20 colonies, vs IMR5-CHD5-AS, 39 colonies, 95% CI = 17 to 60 colonies, P =. 01; tumor growth, n = 10 mice per group: mean tumor size at 5 weeks, NLF-CHD5, 0.36 cm3, 95% CI = 0.17 to 0.44 cm3, vs NLF-CHD5-AS, 1.65 cm3, 95% CI = 0.83 to 2.46 cm3, P =. 002; IMR5-CHD5, 0.28 cm3, 95% CI = 0.18 to 0.38 cm3, vs IMR5-CHD5-AS, 1.15 cm3, 95% CI = 0.43 to 1.87 cm3; P =. 01). High CHD5 expression was strongly associated with favorable event-free and overall survival (P <. 001), even after correction for MYCN amplification and 1p deletion (P =. 027). Conclusions: CHD5 is the strongest candidate tumor suppressor gene that is deleted from 1p36.31 in neuroblastomas, and inactivation of the second allele may occur by an epigenetic mechanism.

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