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SET-NUP214 fusion in acute myeloid leukemia- and T-cell acute lymphoblastic leukemia-derived cell lines.

Quentmeier H, Schneider B, Röhrs S, Romani J, Zaborski M, Macleod RA, Drexler HG - J Hematol Oncol (2009)

Bottom Line: Quantitative genomic PCR also confirmed loss of genomic material between SET and NUP214 in both cell lines.Of special note is that the formation of the SET exon 7/NUP214 exon 18 gene transcript requires alternative splicing as the SET breakpoint is located downstream of the stop codon in exon 8.The cell lines are promising model systems for SET-NUP214 studies and should facilitate investigating cellular functions of the the SET-NUP214 protein.

View Article: PubMed Central - HTML - PubMed

Affiliation: DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany. hqu@dsmz.de

ABSTRACT

Background: SET-NUP214 fusion resulting from a recurrent cryptic deletion, del(9)(q34.11q34.13) has recently been described in T-cell acute lymphoblastic leukemia (T-ALL) and in one case of acute myeloid leukemia (AML). The fusion protein appears to promote elevated expression of HOXA cluster genes in T-ALL and may contribute to the pathogenesis of the disease. We screened a panel of ALL and AML cell lines for SET-NUP214 expression to find model systems that might help to elucidate the cellular function of this fusion gene.

Results: Of 141 human leukemia/lymphoma cell lines tested, only the T-ALL cell line LOUCY and the AML cell line MEGAL expressed the SET(TAF-Ibeta)-NUP214 fusion gene transcript. RT-PCR analysis specifically recognizing the alternative first exons of the two TAF-I isoforms revealed that the cell lines also expressed TAF-Ialpha-NUP214 mRNA. Results of fluorescence in situ hybridization (FISH) and array-based copy number analysis were both consistent with del(9)(q34.11q34.13) as described. Quantitative genomic PCR also confirmed loss of genomic material between SET and NUP214 in both cell lines. Genomic sequencing localized the breakpoints of the SET gene to regions downstream of the stop codon and to NUP214 intron 17/18 in both LOUCY and MEGAL cells. Both cell lines expressed the 140 kDa SET-NUP214 fusion protein.

Conclusion: Cell lines LOUCY and MEGAL express the recently described SET-NUP214 fusion gene. Of special note is that the formation of the SET exon 7/NUP214 exon 18 gene transcript requires alternative splicing as the SET breakpoint is located downstream of the stop codon in exon 8. The cell lines are promising model systems for SET-NUP214 studies and should facilitate investigating cellular functions of the the SET-NUP214 protein.

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Deletion del(9)(q34.11q34.13) in cell lines LOUCY and MEGAL. FISH analysis with BAC clones showed loss of the central (green) signal containing ABL1 and the 5'part of NUP214 in one chromosome 9 homolog in both cell lines. Note that cell line MEGAL carries three copies of chromosome 9.
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Figure 2: Deletion del(9)(q34.11q34.13) in cell lines LOUCY and MEGAL. FISH analysis with BAC clones showed loss of the central (green) signal containing ABL1 and the 5'part of NUP214 in one chromosome 9 homolog in both cell lines. Note that cell line MEGAL carries three copies of chromosome 9.

Mentions: Cell lines are useful model systems to elucidate the cellular function of oncogenes. Therefore, we performed a reverse transcriptase (RT)-PCR based screening of 141 leukemia/lymphoma cell lines of T-, B- and myeloid cell origin to detect SET-NUP214 positive examples. A T-ALL cell line LOUCY (1/43 T cell lines tested) and an AML cell line MEGAL (1/53 myeloid cell lines tested) were the only cell lines expressing the fusion gene. Both cell lines expressed SET exon 7/NUP214 exon 18 fusion mRNA (Fig. 1). SET is the β isoform of TAF-I, differing from TAF-Iα by alternative first exons. RT-PCR with primers recognizing the isoform-specific exons revealed that both cell lines expressed TAF-Iα-NUP214 and TAF-Iβ(SET)-NUP214. Fluorescence in situ hybridization (FISH) analysis with tilepath BAC and fosmid clones (Fig. 2) and array-based copy number analysis revealed del(9)(q34.11q34.13) for LOUCY and MEGAL cells (data not shown). Quantitative genomic PCR confirmed loss of genomic material between SET and NUP214 for both cell lines as indicated by FISH (Fig. 3). Genomic sequencing allocated the centromeric fusion to the untranslated region of SET exon 8 in LOUCY, and to the 3' region of SET in MEGAL, and telomerically to NUP214 intron 17/18 in both cell lines (Fig. 4). Expression of the SET exon 7/NUP214 exon 18 fusion transcript requires alternative splicing: otherwise, full-length SET would be transcribed at the expense of the fusion gene. Alternative splicing as mechanism for SET/NUP214 expression had already been postulated for the first reported case of this fusion gene [6]. Thus, one might speculate that alternative splicing is an obligatory step for SET-NUP214 expression besides the chromosomal aberration itself.


SET-NUP214 fusion in acute myeloid leukemia- and T-cell acute lymphoblastic leukemia-derived cell lines.

Quentmeier H, Schneider B, Röhrs S, Romani J, Zaborski M, Macleod RA, Drexler HG - J Hematol Oncol (2009)

Deletion del(9)(q34.11q34.13) in cell lines LOUCY and MEGAL. FISH analysis with BAC clones showed loss of the central (green) signal containing ABL1 and the 5'part of NUP214 in one chromosome 9 homolog in both cell lines. Note that cell line MEGAL carries three copies of chromosome 9.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2636835&req=5

Figure 2: Deletion del(9)(q34.11q34.13) in cell lines LOUCY and MEGAL. FISH analysis with BAC clones showed loss of the central (green) signal containing ABL1 and the 5'part of NUP214 in one chromosome 9 homolog in both cell lines. Note that cell line MEGAL carries three copies of chromosome 9.
Mentions: Cell lines are useful model systems to elucidate the cellular function of oncogenes. Therefore, we performed a reverse transcriptase (RT)-PCR based screening of 141 leukemia/lymphoma cell lines of T-, B- and myeloid cell origin to detect SET-NUP214 positive examples. A T-ALL cell line LOUCY (1/43 T cell lines tested) and an AML cell line MEGAL (1/53 myeloid cell lines tested) were the only cell lines expressing the fusion gene. Both cell lines expressed SET exon 7/NUP214 exon 18 fusion mRNA (Fig. 1). SET is the β isoform of TAF-I, differing from TAF-Iα by alternative first exons. RT-PCR with primers recognizing the isoform-specific exons revealed that both cell lines expressed TAF-Iα-NUP214 and TAF-Iβ(SET)-NUP214. Fluorescence in situ hybridization (FISH) analysis with tilepath BAC and fosmid clones (Fig. 2) and array-based copy number analysis revealed del(9)(q34.11q34.13) for LOUCY and MEGAL cells (data not shown). Quantitative genomic PCR confirmed loss of genomic material between SET and NUP214 for both cell lines as indicated by FISH (Fig. 3). Genomic sequencing allocated the centromeric fusion to the untranslated region of SET exon 8 in LOUCY, and to the 3' region of SET in MEGAL, and telomerically to NUP214 intron 17/18 in both cell lines (Fig. 4). Expression of the SET exon 7/NUP214 exon 18 fusion transcript requires alternative splicing: otherwise, full-length SET would be transcribed at the expense of the fusion gene. Alternative splicing as mechanism for SET/NUP214 expression had already been postulated for the first reported case of this fusion gene [6]. Thus, one might speculate that alternative splicing is an obligatory step for SET-NUP214 expression besides the chromosomal aberration itself.

Bottom Line: Quantitative genomic PCR also confirmed loss of genomic material between SET and NUP214 in both cell lines.Of special note is that the formation of the SET exon 7/NUP214 exon 18 gene transcript requires alternative splicing as the SET breakpoint is located downstream of the stop codon in exon 8.The cell lines are promising model systems for SET-NUP214 studies and should facilitate investigating cellular functions of the the SET-NUP214 protein.

View Article: PubMed Central - HTML - PubMed

Affiliation: DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany. hqu@dsmz.de

ABSTRACT

Background: SET-NUP214 fusion resulting from a recurrent cryptic deletion, del(9)(q34.11q34.13) has recently been described in T-cell acute lymphoblastic leukemia (T-ALL) and in one case of acute myeloid leukemia (AML). The fusion protein appears to promote elevated expression of HOXA cluster genes in T-ALL and may contribute to the pathogenesis of the disease. We screened a panel of ALL and AML cell lines for SET-NUP214 expression to find model systems that might help to elucidate the cellular function of this fusion gene.

Results: Of 141 human leukemia/lymphoma cell lines tested, only the T-ALL cell line LOUCY and the AML cell line MEGAL expressed the SET(TAF-Ibeta)-NUP214 fusion gene transcript. RT-PCR analysis specifically recognizing the alternative first exons of the two TAF-I isoforms revealed that the cell lines also expressed TAF-Ialpha-NUP214 mRNA. Results of fluorescence in situ hybridization (FISH) and array-based copy number analysis were both consistent with del(9)(q34.11q34.13) as described. Quantitative genomic PCR also confirmed loss of genomic material between SET and NUP214 in both cell lines. Genomic sequencing localized the breakpoints of the SET gene to regions downstream of the stop codon and to NUP214 intron 17/18 in both LOUCY and MEGAL cells. Both cell lines expressed the 140 kDa SET-NUP214 fusion protein.

Conclusion: Cell lines LOUCY and MEGAL express the recently described SET-NUP214 fusion gene. Of special note is that the formation of the SET exon 7/NUP214 exon 18 gene transcript requires alternative splicing as the SET breakpoint is located downstream of the stop codon in exon 8. The cell lines are promising model systems for SET-NUP214 studies and should facilitate investigating cellular functions of the the SET-NUP214 protein.

Show MeSH
Related in: MedlinePlus