A transcript map of the chromosome 19q-arm glioma tumor suppressor region.

Allelic loss of the chromosome 19q arm is a frequent event in human diffuse gliomas, suggesting that it contains a tumor suppressor gene. Recent deletion mapping studies have broadly implicated a 1.6-Mb interval between D19S241E and D19S596, with a limited subset of tumors, suggesting that the region may be as narrow as 150 kb. Focusing on this smaller interval, we have used cDNA selection, exon amplification, and genomic sequencing to identify three novel transcripts (EHD2, GLTSCR1, and GLTSCR2) and to map two known genes (SEPW1 and CRX). A partial transcript map of 19 transcripts and two EST markers has been constructed for the 1.6-Mb interval D19S241E-D19S596. Ten of these transcripts, including the 5 mapped to the 150-kb deletion interval, have been examined for alterations in a panel of gliomas with allelic loss of 19q. Tumor-specific alterations have not been identified in the transcripts examined thus far. Collectively, these data should facilitate subsequent efforts to identify and characterize the remaining transcripts in the 1.6-Mb interval.

Chromosomal localization to 19q13.3, partial genomic structure and 5' cDNA sequence of the human symplekin gene.

Exon trapping from cosmids mapping to chromosome 19q13.3 yielded 6 exonic sequences that matched the human symplekin gene, which encodes a tight junction-related protein. One exonic sequence identified a 4.0 kb brain cDNA clone, R6E1, which contained 302 bp 5' to the originally reported 3.7 kb symplekin cDNA. A portion of this novel 5' sequence matched an additional trapped exonic sequence which was obtained from the most telomeric cosmid analyzed. The symplekin gene thus lies in a telomeric-to-centromeric direction on 19q13.3. Only three cosmids from a large 19q13.3 contig hybridized with R6E1, thereby assigning the symplekin gene to a 40 kb region immediately telomeric to gene 59 and the DM protein kinase gene. The 5' end of the R6E1 clone has a potential initiation codon with a strong Kozak sequence and Northern blot analysis detected a 4.2 kb signal in most human tissues, indicating that R6E1 may be a complete cDNA sequence. Based on the trapped exonic sequences, twelve exon-intron boundaries were predicted.

ANOVA, a putative astrocytic RNA-binding protein gene that maps to chromosome 19q13.3.

Exon amplification from cosmids mapping to the glioma tumor suppressor gene candidate region on chromosome 19q13.3 yielded an exon with high homology to a portion of the NOVA1 gene, which encodes a neuron-specific RNA-binding protein recognized by the paraneoplastic syndrome antibody anti-Ri. Screening of a human brain cDNA library with this exon identified a 1.9 kb cDNA with extensive homology to NOVA1, including three nearly identical KH domains characteristic of a subtype of RNA-binding proteins. Northern blots demonstrated expression of a 2.5 kb mRNA in brain, but in no other tissues. In situ hybridization on human cerebral cortex showed mRNA expression restricted to astrocytes. We have therefore named the gene ANOVA, for astrocytic NOVA1-like gene. Southern blotting and single strand conformation polymorphism analyses did not show tumor-specific alterations of this gene in gliomas and RT-PCR studies showed expression in glioma cell lines, suggesting that ANOVA is not the chromosome 19q glioma tumor suppressor gene. Given that two cloned paraneoplastic antigens are neuronal RNA-binding proteins and that glial proteins may act as paraneoplastic antigens, the ANOVA product may be a target antigen in one of the undefined human paraneoplastic syndromes.