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Genomic cloning of methylthioadenosine phosphorylase: a purine metabolic enzyme deficient in multiple different
T Nobori1, K Takabayashi, P Tran
1The Sam and Rose Stein Institute for Research on Aging, and Department of Medicine, University of California at San Diego, La Jolla, 92093-0663, USA.
Abstract:
5'-Deoxy-5'-methylthioadenosine phosphorylase (methylthioadeno-sine: ortho-phosphate methylthioribosyltransferase, EC 24.2.28; MTAP) plays a role in purine and polyamine metabolism and in the regulation of transmethylation reactions. MTAP is abundant in normal cells but is deficient in many cancers. Recently, the genes for the cyclin-dependent kinase inhibitors p16 and p15 have been localized to the short arm of human chromosome 9 at band p21, where MTAP and interferon alpha genes (IFNA) also map. Homozygous deletions of p16 and p15 are frequent malignant cell lines. However, the order of the MTAP, p16, p15, and IFNA genes on chromosome 9p is uncertain, and the molecular basis for MTAP deficiency in cancer is unknown. We have cloned the MTAP gene, and have constructed a topologic map of the 9p21 region using yeast artificial chromosome clones, pulse-field gel electrophoresis, and sequence-tagged-site PCR. The MTAP gene consists of eight exons and seven introns. Of 23 malignant cell lines deficient in MTAP protein, all but one had complete or partial deletions. Partial or total deletions of the MTAP gene were found in primary T-cell acute lymphoblastic leukemias (T-ALL). A deletion breakpoint of partial deletions found in cell lines and primary T-ALL was in intron 4. Starting from the centromeric end, the gene order on chromosome 9p2l is p15, p16, MTAP, IFNA, and interferon beta gene (IFNB). These results indicate that MTAP deficiency in cancer is primarily due to codeletion of the MTAP and p16 genes.
Insights
5'-Deoxy-5'-methylthioadenosine phosphorylase (MTAP) deficiency is common in cancers due to gene deletions. This study maps the MTAP gene on chromosome 9p21 and reveals its codeletion with p16 in malignant cells.
Area of Science:
- Genetics
- Molecular Biology
- Cancer Research
Background:
- 5'-Deoxy-5'-methylthioadenosine phosphorylase (MTAP) is crucial for purine/polyamine metabolism and transmethylation.
- MTAP is abundant in normal cells but deficient in many cancers.
- Genes p16, p15, MTAP, and IFNA map to chromosome 9p21, a region frequently deleted in malignancies.
Purpose of the Study:
- To determine the gene order of MTAP, p16, p15, and IFNA on chromosome 9p21.
- To investigate the molecular basis of MTAP deficiency in cancer.
- To clone the MTAP gene and map the 9p21 region.
Main Methods:
- Gene cloning of MTAP.
- Topologic mapping of the 9p21 region using yeast artificial chromosome clones.
- Pulse-field gel electrophoresis and sequence-tagged-site PCR.
Main Results:
- The MTAP gene comprises eight exons and seven introns.
- MTAP deficiency in 23 malignant cell lines was associated with complete or partial gene deletions.
- Partial or total MTAP gene deletions were observed in primary T-cell acute lymphoblastic leukemias (T-ALL).
- A deletion breakpoint was identified in intron 4 of the MTAP gene.
- The gene order on chromosome 9p21 was established as p15, p16, MTAP, IFNA, and IFNB.
Conclusions:
- MTAP deficiency in cancer is primarily caused by the codeletion of the MTAP and p16 genes.
- Understanding gene order on chromosome 9p21 clarifies the genetic basis of MTAP deficiency in various cancers.