A novel gene, NSD1, is fused to NUP98 in the t(5;11)(q35;p15.5) in de novo childhood acute myeloid leukemia.

The recurrent translocation t(5;11)(q35;p15.5) associated with a 5q deletion, del(5q), has been reported in childhood acute myeloid leukemia (AML). We report the cloning of the translocation breakpoints in de novo childhood AML harboring a cryptic t(5;11)(q35;p15.5). Fluorescence in situ hybridization (FISH) analysis demonstrated that the nucleoporin gene (NUP98) at 11p15.5 was disrupted by this translocation. By using 3'--rapid amplification of complementary DNA ends (3'-RACE) polymerase chain reaction, we identified a chimeric messenger RNA that results in the in-frame fusion of NUP98 to a novel gene, NSD1. The NSD1 gene has 2596 amino acid residues and a 85% homology to the murine Nsd1 with the domain structure being conserved. The NSD1 gene was localized to 5q35 by FISH and is widely expressed. The reciprocal transcript, NSD1-NUP98, was also detected by reverse transcriptase--polymerase chain reaction. This is the first report in which the novel gene NSD1 has been implicated in human malignancy. (Blood. 2001;98:1264-1267)

Physical mapping of the human ATX1 homologue (HAH1) to the critical region of the 5q- syndrome within 5q32, and immediately adjacent to the SPARC gene.

The 5q- syndrome is a myelodysplastic syndrome with the 5q deletion as the sole karyotypic abnormality. The human ATX1 homologue (HAH1), encodes a copper-binding protein with a role in antioxidant defence. We have mapped this gene to the 3 Mb critical region of gene loss of the 5q- syndrome within 5q32, flanked by the genes for ADRB2 and IL12B, using gene dosage analysis. Fine physical mapping of the HAH1 gene within this genomic interval was then performed by screening YAC and BAC contigs spanning the critical region of the 5q- syndrome using PCR amplification. The HAH1 gene maps immediately adjacent to the SPARC gene at 5q32, and is flanked by the genetic markers D5S1838 and D5S1419. The HAH1 gene is expressed in haematological tissues and plays a role in antioxidant defence. Antioxidant levels are low in most cancers and the importance of antioxidant enzymes in cancer genesis is well recognised. Genomic localisation, function and expression would suggest that the HAH1 gene represents a candidate gene for the 5q-syndrome.

Transcription mapping of the 5q- syndrome critical region: cloning of two novel genes and sequencing, expression, and mapping of a further six novel cDNAs.

The 5q- syndrome is a myelodysplastic syndrome with the 5q deletion ¿del(5q) as the sole karyotypic abnormality. We are using the expressed sequence tag (EST) resource as our primary approach to identifying novel candidate genes for the 5q- syndrome. Seventeen ESTs were identified from the Human Gene Map at the National Center for Biotechnology Information that had no significant homology to any known genes and were assigned between DNA markers D5S413 and D5S487, flanking the critical region of the 5q- syndrome at 5q31-q32. Eleven of the 17 cDNAs from which the ESTs were derived (65%) were shown to map to the critical region of the 5q- syndrome by gene dosage analysis and were then sublocalized by PCR screening to a YAC contig encompassing the critical region. Eight of the 11 cDNA clones, upon full sequencing, had no significant homology to any known genes. Each of the 8 cDNA clones was shown to be expressed in human bone marrow. The complete coding sequence was obtained for 2 of the novel genes, termed C5orf3 and C5orf4. The 2.6-kb transcript of C5orf3 encodes a putative 505-amino-acid protein and contains an ATP/GTP-binding site motif A (P loop), suggesting that this novel gene encodes an ATP- or a GTP-binding protein. The novel gene C5orf4 has a transcript of 3.1 kb, encoding a putative 144-amino-acid protein. We describe the cloning of 2 novel human genes and the sequencing, expression patterns, and mapping to the critical region of the 5q- syndrome of a further 6 novel cDNA clones. Genomic localization and expression patterns would suggest that the 8 novel cDNAs described in this report represent potential candidate genes for the 5q- syndrome.

Novel genes mapping to the critical region of the 5q- syndrome.

The 5q- syndrome is a myelodysplastic syndrome with specific hematological features and a good prognosis. Using molecular mapping techniques, we have previously defined the critical region of gene loss of the 5q- chromosome in the 5q- syndrome as the approximately 5-Mb region at 5q31-q33 flanked by the genes for FGF1 and IL12B. This region is completely represented by a series of overlapping YACs, and we are currently generating a transcription map with the aim of identifying the tumor-suppressor gene associated with the development of the 5q- syndrome. In this study two techniques have been used: first, the screening of full-length cDNA libraries with radiolabeled YACs and second, the mapping of chromosome 5-specific expressed sequence tags (ESTs) to a YAC contig. A 1-Mb YAC contig encompassing the CSF1R gene has been used to screen a fetal brain cDNA library, and this has resulted in the identification of two genes comprising one known gene previously localized to the region (ADRB2) and one known gene previously unlocalized. Six of 135 chromosome 5-specific ESTs were localized by PCR screening to the YAC contig mapping to the critical region of the 5q- syndrome. IMAGE cDNA clones for each of the six ESTs have been obtained. These seven (excluding ADRB2) newly assigned cDNA clones were subjected to further analysis. The expression patterns of each of the cDNA clones have been established in a range of human tissues, including bone marrow. Six of seven cDNAs are expressed in human bone marrow. Six of seven cDNAs have no known homology to any deposited human sequences, and one (C29) is dihydropyrimidinase-related protein-3, a member of a novel gene family. Genomic localization and expression patterns would suggest that these newly assigned cDNAs represent potential candidate genes for the 5q- syndrome.