Identification and characterization of a 500-kb homozygously deleted region at 1p36.2-p36.3 in a neuroblastoma cell line

Miki Ohira, Hajime Kageyama, Motohiro Mihara, Shigeyuki Furuta, Taiichi Machida, Tomotane Shishikura, Hajime Takayasu, Ashraful Islam, Yohko Nakamura, Masato Takahashi, Nobumoto Tomioka, Shigeru Sakiyama, Yasuhiko Kaneko, Atsushi Toyoda, Masahira Hattori, Yoshiyuki Sakaki, Misao Ohki, Akira Horii, Eiichi Soeda, Johji Inazawa & 4 others Naohiko Seki, Hidekazu Kuma, Iwao Nozawa, Akira Nakagawara

Research output: Contribution to journalArticle

69 Citations (Scopus)

Abstract

Loss of heterozygosity of the distal region of chromosome 1p where tumor suppressor gene(s) might harbor is frequently observed in many human cancers including neuroblastoma (NBL) with MYCN amplification and poor prognosis. We have identified for the first time a homozygously deleted region at the marker D1S244 within the smallest region of overlap at 1p36.2-p36.3 in two NBL cell lines, NB-1 and NB-C201 (MASS-NB-SCH1), although our genotyping has suggested the possibility that both lines are derived from the same origin. The 800-kb PAC contig covering the entire region of homozygous deletion was made and partially sequenced (about 60%). The estimated length of the deleted region was 500 kb. We have, thus far, identified six genes within the region which include three known genes (DFF45, PGD, and CORT) as well as three other genes which have been reported during processing our present project for the last 3 1/2 years (HDNB1/UFD2, KIAAO591F/KIF1B-β, and PEX14). They include the genes related to apoptosis, glucose metabolism, ubiquitin-proteasome pathway, a neuronal microtubule-associated motor molecule and biogenesis of peroxisome. At least three genes (HDNB1/UFD2, KIAAO591F/KIF1B-β, and PEX14) were differentially expressed at high levels in favorable and at low levels in unfavorable subsets of primary neuroblastoma. Since the 1p distal region is reported to be imprinted, those differentially expressed genes could be the new members of the candidate NBL suppressor, although RT-PCR-SSCP analysis has demonstrated infrequent mutation of the genes so far identified. Full-sequencing and gene prediction for the region of homozygous deletion would elucidate more detailed structure of this region and might lead to discovery of additional candidate genes.

Original languageEnglish
Pages (from-to)4302-4307
Number of pages6
JournalOncogene
Volume19
Issue number37
Publication statusPublished - 2000 Aug 31
Externally publishedYes

Fingerprint

Neuroblastoma
Cell Line
Genes
Prostaglandins D
Single-Stranded Conformational Polymorphism
Peroxisomes
Loss of Heterozygosity
Proteasome Endopeptidase Complex
Ubiquitin
Tumor Suppressor Genes
Microtubules
Chromosomes
Apoptosis
Glucose
Polymerase Chain Reaction
Mutation

Keywords

  • 1p36
  • Homozygous deletion
  • Neuroblastoma
  • Tumor suppressor gene

ASJC Scopus subject areas

  • Molecular Biology
  • Cancer Research
  • Genetics

Cite this

Ohira, M., Kageyama, H., Mihara, M., Furuta, S., Machida, T., Shishikura, T., ... Nakagawara, A. (2000). Identification and characterization of a 500-kb homozygously deleted region at 1p36.2-p36.3 in a neuroblastoma cell line. Oncogene, 19(37), 4302-4307.

Identification and characterization of a 500-kb homozygously deleted region at 1p36.2-p36.3 in a neuroblastoma cell line. / Ohira, Miki; Kageyama, Hajime; Mihara, Motohiro; Furuta, Shigeyuki; Machida, Taiichi; Shishikura, Tomotane; Takayasu, Hajime; Islam, Ashraful; Nakamura, Yohko; Takahashi, Masato; Tomioka, Nobumoto; Sakiyama, Shigeru; Kaneko, Yasuhiko; Toyoda, Atsushi; Hattori, Masahira; Sakaki, Yoshiyuki; Ohki, Misao; Horii, Akira; Soeda, Eiichi; Inazawa, Johji; Seki, Naohiko; Kuma, Hidekazu; Nozawa, Iwao; Nakagawara, Akira.

In: Oncogene, Vol. 19, No. 37, 31.08.2000, p. 4302-4307.

Research output: Contribution to journalArticle

Ohira, M, Kageyama, H, Mihara, M, Furuta, S, Machida, T, Shishikura, T, Takayasu, H, Islam, A, Nakamura, Y, Takahashi, M, Tomioka, N, Sakiyama, S, Kaneko, Y, Toyoda, A, Hattori, M, Sakaki, Y, Ohki, M, Horii, A, Soeda, E, Inazawa, J, Seki, N, Kuma, H, Nozawa, I & Nakagawara, A 2000, 'Identification and characterization of a 500-kb homozygously deleted region at 1p36.2-p36.3 in a neuroblastoma cell line', Oncogene, vol. 19, no. 37, pp. 4302-4307.
Ohira M, Kageyama H, Mihara M, Furuta S, Machida T, Shishikura T et al. Identification and characterization of a 500-kb homozygously deleted region at 1p36.2-p36.3 in a neuroblastoma cell line. Oncogene. 2000 Aug 31;19(37):4302-4307.
Ohira, Miki ; Kageyama, Hajime ; Mihara, Motohiro ; Furuta, Shigeyuki ; Machida, Taiichi ; Shishikura, Tomotane ; Takayasu, Hajime ; Islam, Ashraful ; Nakamura, Yohko ; Takahashi, Masato ; Tomioka, Nobumoto ; Sakiyama, Shigeru ; Kaneko, Yasuhiko ; Toyoda, Atsushi ; Hattori, Masahira ; Sakaki, Yoshiyuki ; Ohki, Misao ; Horii, Akira ; Soeda, Eiichi ; Inazawa, Johji ; Seki, Naohiko ; Kuma, Hidekazu ; Nozawa, Iwao ; Nakagawara, Akira. / Identification and characterization of a 500-kb homozygously deleted region at 1p36.2-p36.3 in a neuroblastoma cell line. In: Oncogene. 2000 ; Vol. 19, No. 37. pp. 4302-4307.
@article{17ecddcc61a24e77923e4c3170bc3310,
title = "Identification and characterization of a 500-kb homozygously deleted region at 1p36.2-p36.3 in a neuroblastoma cell line",
abstract = "Loss of heterozygosity of the distal region of chromosome 1p where tumor suppressor gene(s) might harbor is frequently observed in many human cancers including neuroblastoma (NBL) with MYCN amplification and poor prognosis. We have identified for the first time a homozygously deleted region at the marker D1S244 within the smallest region of overlap at 1p36.2-p36.3 in two NBL cell lines, NB-1 and NB-C201 (MASS-NB-SCH1), although our genotyping has suggested the possibility that both lines are derived from the same origin. The 800-kb PAC contig covering the entire region of homozygous deletion was made and partially sequenced (about 60{\%}). The estimated length of the deleted region was 500 kb. We have, thus far, identified six genes within the region which include three known genes (DFF45, PGD, and CORT) as well as three other genes which have been reported during processing our present project for the last 3 1/2 years (HDNB1/UFD2, KIAAO591F/KIF1B-β, and PEX14). They include the genes related to apoptosis, glucose metabolism, ubiquitin-proteasome pathway, a neuronal microtubule-associated motor molecule and biogenesis of peroxisome. At least three genes (HDNB1/UFD2, KIAAO591F/KIF1B-β, and PEX14) were differentially expressed at high levels in favorable and at low levels in unfavorable subsets of primary neuroblastoma. Since the 1p distal region is reported to be imprinted, those differentially expressed genes could be the new members of the candidate NBL suppressor, although RT-PCR-SSCP analysis has demonstrated infrequent mutation of the genes so far identified. Full-sequencing and gene prediction for the region of homozygous deletion would elucidate more detailed structure of this region and might lead to discovery of additional candidate genes.",
keywords = "1p36, Homozygous deletion, Neuroblastoma, Tumor suppressor gene",
author = "Miki Ohira and Hajime Kageyama and Motohiro Mihara and Shigeyuki Furuta and Taiichi Machida and Tomotane Shishikura and Hajime Takayasu and Ashraful Islam and Yohko Nakamura and Masato Takahashi and Nobumoto Tomioka and Shigeru Sakiyama and Yasuhiko Kaneko and Atsushi Toyoda and Masahira Hattori and Yoshiyuki Sakaki and Misao Ohki and Akira Horii and Eiichi Soeda and Johji Inazawa and Naohiko Seki and Hidekazu Kuma and Iwao Nozawa and Akira Nakagawara",
year = "2000",
month = "8",
day = "31",
language = "English",
volume = "19",
pages = "4302--4307",
journal = "Oncogene",
issn = "0950-9232",
publisher = "Nature Publishing Group",
number = "37",

}

TY - JOUR

T1 - Identification and characterization of a 500-kb homozygously deleted region at 1p36.2-p36.3 in a neuroblastoma cell line

AU - Ohira, Miki

AU - Kageyama, Hajime

AU - Mihara, Motohiro

AU - Furuta, Shigeyuki

AU - Machida, Taiichi

AU - Shishikura, Tomotane

AU - Takayasu, Hajime

AU - Islam, Ashraful

AU - Nakamura, Yohko

AU - Takahashi, Masato

AU - Tomioka, Nobumoto

AU - Sakiyama, Shigeru

AU - Kaneko, Yasuhiko

AU - Toyoda, Atsushi

AU - Hattori, Masahira

AU - Sakaki, Yoshiyuki

AU - Ohki, Misao

AU - Horii, Akira

AU - Soeda, Eiichi

AU - Inazawa, Johji

AU - Seki, Naohiko

AU - Kuma, Hidekazu

AU - Nozawa, Iwao

AU - Nakagawara, Akira

PY - 2000/8/31

Y1 - 2000/8/31

N2 - Loss of heterozygosity of the distal region of chromosome 1p where tumor suppressor gene(s) might harbor is frequently observed in many human cancers including neuroblastoma (NBL) with MYCN amplification and poor prognosis. We have identified for the first time a homozygously deleted region at the marker D1S244 within the smallest region of overlap at 1p36.2-p36.3 in two NBL cell lines, NB-1 and NB-C201 (MASS-NB-SCH1), although our genotyping has suggested the possibility that both lines are derived from the same origin. The 800-kb PAC contig covering the entire region of homozygous deletion was made and partially sequenced (about 60%). The estimated length of the deleted region was 500 kb. We have, thus far, identified six genes within the region which include three known genes (DFF45, PGD, and CORT) as well as three other genes which have been reported during processing our present project for the last 3 1/2 years (HDNB1/UFD2, KIAAO591F/KIF1B-β, and PEX14). They include the genes related to apoptosis, glucose metabolism, ubiquitin-proteasome pathway, a neuronal microtubule-associated motor molecule and biogenesis of peroxisome. At least three genes (HDNB1/UFD2, KIAAO591F/KIF1B-β, and PEX14) were differentially expressed at high levels in favorable and at low levels in unfavorable subsets of primary neuroblastoma. Since the 1p distal region is reported to be imprinted, those differentially expressed genes could be the new members of the candidate NBL suppressor, although RT-PCR-SSCP analysis has demonstrated infrequent mutation of the genes so far identified. Full-sequencing and gene prediction for the region of homozygous deletion would elucidate more detailed structure of this region and might lead to discovery of additional candidate genes.

AB - Loss of heterozygosity of the distal region of chromosome 1p where tumor suppressor gene(s) might harbor is frequently observed in many human cancers including neuroblastoma (NBL) with MYCN amplification and poor prognosis. We have identified for the first time a homozygously deleted region at the marker D1S244 within the smallest region of overlap at 1p36.2-p36.3 in two NBL cell lines, NB-1 and NB-C201 (MASS-NB-SCH1), although our genotyping has suggested the possibility that both lines are derived from the same origin. The 800-kb PAC contig covering the entire region of homozygous deletion was made and partially sequenced (about 60%). The estimated length of the deleted region was 500 kb. We have, thus far, identified six genes within the region which include three known genes (DFF45, PGD, and CORT) as well as three other genes which have been reported during processing our present project for the last 3 1/2 years (HDNB1/UFD2, KIAAO591F/KIF1B-β, and PEX14). They include the genes related to apoptosis, glucose metabolism, ubiquitin-proteasome pathway, a neuronal microtubule-associated motor molecule and biogenesis of peroxisome. At least three genes (HDNB1/UFD2, KIAAO591F/KIF1B-β, and PEX14) were differentially expressed at high levels in favorable and at low levels in unfavorable subsets of primary neuroblastoma. Since the 1p distal region is reported to be imprinted, those differentially expressed genes could be the new members of the candidate NBL suppressor, although RT-PCR-SSCP analysis has demonstrated infrequent mutation of the genes so far identified. Full-sequencing and gene prediction for the region of homozygous deletion would elucidate more detailed structure of this region and might lead to discovery of additional candidate genes.

KW - 1p36

KW - Homozygous deletion

KW - Neuroblastoma

KW - Tumor suppressor gene

UR - http://www.scopus.com/inward/record.url?scp=0034738963&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0034738963&partnerID=8YFLogxK

M3 - Article

VL - 19

SP - 4302

EP - 4307

JO - Oncogene

JF - Oncogene

SN - 0950-9232

IS - 37

ER -