Comparative genomic hybridization study of nasal‐type NK/T‐cell lymphoma

Ko, Young Hyeh; Choi, Kyung Jun; Han, Joung-Ho; Kim, Jin M.; Ree, H. J.

doi:10.1002/cyto.1069

Cited by 57 publications

(49 citation statements)

References 23 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Del 6q was the most frequent loss as in earlier studies 4,6,8 and four distinct regions: 6q21, 6q23.2, 6q25.3 and 6q26 have been suggested. 7,10,11,21,39 Previous results and our data suggest that 6q21 (B105.6-107 Mb) is the most common aberrant region (Table 1a).…”

Section: Genomic Studies On Natural Killer-cell Malignancies J Iqbal supporting

confidence: 61%

“…6 We did not attempt to divide our cases into subcategories of NK-cell malignancies due to the small number of samples, but instead focused on abnormalities that are commonly present and probably important in the pathogenesis of NK-cell malignancies. Consolidating data from other studies 4,6,8 points to gains in 1q, 7q35, 17q21.2 and 20q11.1 are the most frequent. We examined the expression of 41000 transcripts residing in these regions and found that generally 30-50% of genes in these aberrant regions showed increase in expression compared with cases without the gains.…”

Section: Genomic Studies On Natural Killer-cell Malignancies J Iqbal mentioning

confidence: 89%

“…To compare our findings with previous published data, we assembled all CGH data through an extensive literature search [4][5][6][7][8][9][10][11]21 that included three studies: conventional CGH on 9 Korean patients, 4 conventional CGH on 10 Chinese patients 8 and aCGH on 27 Japanese patients. 6 We also included other reports with cytogenetics, loss of heterozygosity (LOH) and fluorescent in situ hybridization data on 15 cases of NK-cell malignancies.…”

Section: Discussionmentioning

confidence: 99%

“…Only a few studies of genome-wide alterations have been published on NK-cell malignancies [4][5][6][7][8][9][10][11] due to the rarity of this entity and the difficulty in obtaining adequate biopsy specimens. Therefore, well-characterized NK cell lines, supplemented with tumor specimens, can have an important role in the investigation of NK-cell malignancies.…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Genomic analyses reveal global functional alterations that promote tumor growth and novel tumor suppressor genes in natural killer-cell malignancies

Iqbal

Küçük

deLeeuw³

et al. 2009

Leukemia

173

199

View full text Add to dashboard Cite

Natural killer (NK)-cell malignancies are among the most aggressive lymphoid neoplasms with very poor prognosis. We performed array comparative genomic hybridization analysis on a number of NK cell lines and primary tumors to gain better understanding of the pathogenesis and tumor biology of these malignancies. We also obtained transcriptional profiles of genes residing in these regions and compared them with normal and activated NK cells. Only 30-50% of the genes residing in the gained or deleted regions showed corresponding increased or decreased expression. However, many of the upregulated genes in regions of gain are functionally important for the proliferation and growth of the neoplastic population. Genes downregulated in regions of loss included many transcription factors or repressors, tumor suppressors or negative regulators of the cell cycle. The minimal common region of deletion in 6q21 included three known genes (PRDM1, ATG5 and AIM1) showing generally low expression. Mutations resulting in truncated PRDM1 and changes in conserved amino-acid sequences of AIM1 were detected. Highly methylated CpG islands 5 0 of PRDM1 and AIM1 correlated with low expression of the transcripts. Reversal of methylation by Decitabine induced expression of PRDM1 and cell death. In conclusion, we have shown a general tumorpromoting effect of genetic alterations and have identified PRDM1 as the most likely target gene in del6q21. ATG5, an essential gene for autophagy and AIM1, a gene implicated in melanoma, may also participate in the functional abnormalities.

show abstract

Section: Genomic Studies On Natural Killer-cell Malignancies J Iqbal supporting

confidence: 61%

Section: Genomic Studies On Natural Killer-cell Malignancies J Iqbal mentioning

confidence: 89%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Genomic analyses reveal global functional alterations that promote tumor growth and novel tumor suppressor genes in natural killer-cell malignancies

Iqbal

Küçük

deLeeuw³

et al. 2009

Leukemia

173

199

View full text Add to dashboard Cite

show abstract

“…Amplification at 13q21-qter has been reported in diffuse large B-cell lymphoma (DLBCL; Ref. 5), mantle cell lymphoma (6), follicular lymphoma (7), primary cutaneous B-cell lymphoma (8), and nasal-type natural killer/T-cell lymphoma (9). Additional cases of amplification at 13q21-qter have also been reported in solid tumors: glioma (10), non-small cell lung cancer (10), bladder cancer (10), squamous-cell carcinoma of the head and neck (10), peripheral nerve sheath tumor (11), malignant fibrous histiocytoma (12), and alveolar rhabdomyosarcoma (13).…”

Section: Introductionmentioning

confidence: 99%

Identification and Characterization of a Novel Gene, C13orf25 , as a Target for 13q31-q32 Amplification in Malignant Lymphoma

et al. 2004

View full text Add to dashboard Cite

The amplification at 13q31-q32 has been reported in not only hematopoietic malignancies but also in other solid tumors. We identified previously frequent amplification of chromosomal band 13q31-q32 in 70 cases of diffuse large B-cell lymphoma patients by conventional comparative genomic hybridization analysis. In an attempt to identify a candidate gene within this region, we used array comparative genomic hybridization and fluorescent in situ hybridization to map the 13q31-q32 amplicon. We then screened the 65 expressed sequence tags and Glypican 5 (GPC5) by reverse transcription-PCR and Northern blotting. As a result, we identified a novel gene, designated Chromosome 13 open reading frame 25 (C13orf25), which was overexpressed in B-cell lymphoma cell lines and diffuse large B-cell lymphoma patients with 13q31-q32 amplifications. However, GPC5, which has been reported to be a target gene for 13q31-q32 amplification, was truncated in one cell line, Rec1, possessing the amplification, and its expression in various cell lines with amplification at 13q31-q32 was not significantly different from that in other cell lines without amplification, suggesting that GPC5 is not likely to be the candidate gene. Additional analysis identified two major transcripts in the C13orf25 gene. The two transcripts A and B predicted open reading frames of 32 and 70-amino acid polypeptides, respectively. The former has been reported as bA121J7.2, which is conserved among species. Transcript-B also contained seven mature microRNAs in its untranslated region. These results suggest that the C13orf25 gene is the most likely candidate gene for the 13q31-q32 amplicon found in hematopoietic malignancies.

show abstract

Gene expression analysis of chromosomal regions with gain or loss of genetic material detected by comparative genomic hybridization

Meléndez

Dı́az-Uriarte

Cuadros

et al. 2004

Genes Chromosomes & Cancer

View full text Add to dashboard Cite

Comparative genomic hybridization (CGH) has been widely used to detect copy number alterations in cancer and to identify regions containing candidate tumor-responsible genes; however, gene expression changes have been described only in highly amplified regions (amplicons). To study the overall impact of slight copy number changes on gene expression, we analyzed 16 T-cell lymphomas by using CGH and a custom-designed cDNA microarray containing 7,657 genes and expressed sequence tags related to tumorigenesis. We evaluated mean gene expression and variability within CGH-altered regions and explored the relationship between the effects of the gene and its position within these regions. Minimally overlapping CGH candidate areas (6q25, 13q21-q22, and 19q13.1) revealed a weak relationship between altered genomic content and gene expression. However, some candidate genes showed modified expression within these regions in the majority of tumors; these candidate genes were evaluated and confirmed in another independent series of 23 T-cell lymphomas by use of the same cDNA microarray and by FISH on a tissue microarray. When all the CGH regions detected for each tumor were considered, we found a significant increase or decrease in the mean expression of the genes contained in gained or lost regions, respectively. In addition, we found that the expression of a gene was dependent not only on its position within an altered region but also on its own mechanism of regulation: genes in the same altered region responded very differently to the gain or loss of genetic material. Supplementary material for this article can be found on the Genes, Chromosomes, and Cancer website at http://www.interscience.wiley.com/jpages/1045-2257/suppmat/index.html.

show abstract

Comparative genomic hybridization study of nasal‐type NK/T‐cell lymphoma

Cited by 57 publications

References 23 publications

Genomic analyses reveal global functional alterations that promote tumor growth and novel tumor suppressor genes in natural killer-cell malignancies

Genomic analyses reveal global functional alterations that promote tumor growth and novel tumor suppressor genes in natural killer-cell malignancies

Identification and Characterization of a Novel Gene, C13orf25 , as a Target for 13q31-q32 Amplification in Malignant Lymphoma

Gene expression analysis of chromosomal regions with gain or loss of genetic material detected by comparative genomic hybridization

Contact Info

Product

Resources

About