Faculty Bibliography

Meningioma is a frequently occurring tumor of the meninges surrounding the central nervous system. Loss of the short arm of chromosome 1 (1p) is the second most frequent chromosomal abnormality observed in these tumors. Previously, we identified a 3.7 megabase (Mb) region of consistent deletion on 1p33-p34 in a panel of 157 tumors. Loss of this region was associated with advanced disease and predictive for tumor relapse. In this report, a high-resolution integrated map of the region was constructed (CompView) to identify all markers in the smallest region of overlapping deletion (SRO). A regional somatic cell hybrid panel was used to more precisely localize those markers identified in CompView as within or overlapping the region. Additional deletion mapping using microsatellites localized to the region narrowed the SRO to approximately 2.8 Mb. The 88 markers remaining in the SRO were used to screen genomic databases to identify large-insert clones. Clones were assembled into a physical map of the region by PCR-based, sequence-tagged site (STS) content mapping. A sequence from clones was used to validate STS content by electronic PCR and to identify transcripts. A minimal tiling path of 43 clones was constructed across the SRO. Sequence data from the most current sequence assembly were used for further validation. A total of 59 genes were ordered within the SRO. In all, 17 of these were selected as likely candidates based on annotation using Gene Ontology Consortium terms, including the MUTYH, PRDX1, FOXD2, FOXE3, PTCH2, and RAD54L genes. This annotation of a putative tumor suppressor locus provides a resource for further analysis of meningioma candidate genes.

Marker positions on nine genetic linkage, radiation hybrid, and integrated maps of human chromosome 22 were compared with their corresponding positions in the completed DNA sequence. The proportion of markers whose map position is <250 kb from their respective sequence positions ranges from 100% to 35%. Several discordant markers were identified, as well as four regions that show common inconsistencies across multiple maps. These shared discordant regions surround duplicated DNA segments and may indicate mapping or assembly errors due to sequence homology. Recombination-rate distributions along the chromosome were also evaluated, with male and female meioses showing significantly different patterns of recombination, including an 8-Mb male recombination desert. The distributions of radiation-induced chromosome breakage for the GB4 and the G3 radiation hybrid panels were also evaluated. Both panels show fluctuations in breakage intensity, with different regions of significantly elevated rates of breakage. These results provide support for the common assumption that radiation-induced breaks are generally randomly distributed. The present studies detail the limitations of these important map resources and should prove useful for clarifying potential problems in the human maps and sequence assemblies, as well as for mapping and sequencing projects in and across other species.

BACKGROUND:Several lines of evidence es tablish that chromosome band 1p36 is frequently deleted in neuroblastoma primary tumors and cell lines, suggesting that a tumor suppressor gene within this region is involved in the development of this tumor. PROCEDURE/METHODS:We analyzed the status of 1p36 in primary neuroblastomas and cell lines to define the region of consistent rearrangement. RESULTS:Loss of heterozygosity (LOH) studies of primary neuro blastomas identified allelic loss in 135 of 503 tumors (27%), with the smallest region of overlap (SRO) defined distal to D15214 (1p36.3). No homozygous deletions were detected at 120 loci mapping to 1p36.1-p36.3 in a panel of 46 neuroblastoma cell lines. A recently identified patient with neuroblastoma was found to have a constitutional deletion within 1p36.2-p36.3, and this deletion, when combined with the LOH results, defined a smaller SRO of one megabase within 1p36.3. We constructed a comprehensive integrated map of chromosome 1 containing 11,000 markers and large-insert clones, a high-resolution radiation hybrid (RH) map of 1p36, and a P1-artificial chromosome (PAC) contig spanning the SRO, to further characterize the region of interest. Over 768 kb (75%) of the SRO has been sequenced to completion. Further analysis of distal 1p identified 113 transcripts localizing to 1p36, 21 of which were mapped within the SRO. CONCLUSION/CONCLUSIONS:This analysis will identify suitable positional candidate transcripts for mutational screening and subsequent identification of the 1p36.3 neuroblastoma suppressor gene.

BACKGROUND:Deletion of the distal short arm of chromosome 1 occurs frequently in neuroblastoma. In addition, neuroblastoma has been described in children with constitutional deletions within 1p36, supporting the existence of one or more neuroblastoma suppressor genes within this region. PROCEDURE/METHODS:We have pursued a 1p36 tumor suppressor gene identification strategy that has included deletion mapping of 566 primary neuroblastomas and 46 neuroblastoma-derived cell lines, and have determined the parental origin of the deleted 1p homologue in 44 cases to determine whether there is evidence for genomic imprinting within this region. RESULTS AND CONCLUSIONS/CONCLUSIONS:We have identified a 1-Mb consensus region of deletion within 1p36.3 defined by primary tumor deletions, constructed a physical map of the region that is being sequenced to completion, and have identified and prioritized candidate genes within this region for further analyses.

BACKGROUND:MYCN amplification and overexpression occurs in 25% of neuroblastomas and independently predicts for poor prognosis disease, an effect thought to be mediated by its role as a transcriptional activator of growth promoting genes. However, in many mammalian cells, deregulated expression of MYC family genes (including MYCN) induces apoptosis. We hypothesized that BIN1, a MYC interacting protein capable of inducing apoptosis, may be an important regulator of MYCN in neuroblastoma. RESULTS:BIN1 expression was found to be reduced in MYCN-amplified cell lines. Further, forced expression of BIN1 markedly reduced colony formation in MYCN-amplified, but not single-copy, cell lines. This effect appeared to be caused by an increase in apoptosis, and was augmented by serum deprivation and concurrent cytotoxic drug therapy in cell culture CONCLUSION/CONCLUSIONS:BIN1 inactivation may be necessary for MYCN overexpression to lead to cellular proliferation rather than programmed cell death in neuroblastomas with MYCN amplification.

PURPOSE/OBJECTIVE:To determine the independent prognostic significance of 1p36 loss of heterozygosity (LOH) in a representative group of neuroblastoma patients. PATIENTS AND METHODS/METHODS:Diagnostic tumor specimens from 238 patients registered onto the most recent Children's Cancer Group phase III clinical trials were assayed for LOH with 13 microsatellite polymorphic markers spanning chromosome band 1p36. Allelic status at 1p36 was correlated with other prognostic variables and disease outcome. RESULTS:LOH at 1p36 was detected in 83 (35%) of 238 neuroblastomas. There was a correlation of 1p36 LOH with age at diagnosis greater than 1 year (P = .026), metastatic disease (P<.001), elevated serum ferritin level (P<.001), unfavorable histopathology (P<.001), and MYCN oncogene amplification (P<.001). LOH at 1p36 was associated with decreased event-free survival (EFS) and overall survival (OS) probabilities (P<.0001). For the 180 cases with single-copy MYCN, 1p36 LOH status was highly correlated with decreased EFS (P = .0002) but not OS (P = .1212). Entering 1p36 LOH into a multivariate regression model suggested a trend toward an independent association with decreased EFS (P = .0558) but not with decreased OS (P = .3687). Furthermore, allelic status at 1p36 was the only prognostic variable that was significantly associated with decreased EFS in low-risk neuroblastoma patients (P = .0148). CONCLUSION/CONCLUSIONS:LOH at 1p36 is independently associated with decreased EFS, but not OS, in neuroblastoma patients. Determination of 1p36 allelic status may be useful for predicting which neuroblastoma patients with otherwise favorable clinical and biologic features are more likely to have disease progression.

Comprehensive representations of human chromosomes combining diverse genomic data sets, localizing expressed sequences, and reflecting physical distance are essential for disease gene identification and sequencing efforts. We have developed a method (CompView) for integrating genomic information derived from available cytogenetic, genetic linkage, radiation hybrid, physical, and transcript-based mapping approaches. CompView generates chromosome representations with substantially higher resolution, coverage, and integration than current maps of the human genome. The CompView process was used to build a representation of human chromosome 1, yielding a map with >13,000 unique elements, an effective resolution of 910 kb, and a marker density of 50 kb. CompView creates comprehensive and fully integrated depictions of a chromosome's clinical, biological, and structural information.

Neuroblastoma is a pediatric malignancy of the sympathetic nervous system and is frequently characterized by genetic aberrations (including aneuploidy, chromosomal deletions, translocations, and gene amplification) that suggest inherent genomic instability. Mutations in mismatch repair (MMR) genes have been associated with genomic instability in several human cancers, such as those of the hereditary nonpolyposis colorectal cancer (HNPCC) syndrome. In these cases, replication errors at microsatellite repeats lead to microsatellite instability (MSI) and mutagenesis. In neuroblastoma, we and others have detected MSI infrequently when analyzed at di- or tetranucleotide repeat polymorphic markers. More recently, however, mutations in the MMR gene GTBP/hMSH6 have been associated with a limited phenotype of instability at mononucleotide repeats only (e.g., polyadenine tracts). Furthermore, mononucleotide repeats appear to be common downstream targets of MSI-related mutagenesis and are present in the transforming growth factor-beta receptor-II gene (TGF beta RII), the BAX proapoptosis gene, and the insulin-like growth factor II receptor gene (IGFIIR) frequently in tumors arising in HNPCC kindreds. Therefore, we analyzed 46 matched normal and tumor DNAs representing all clinical stages of neuroblastoma with the use of five polymorphic mononucleotide repeat markers to assess for MSI at mononucleotide repeats. Only one tumor (2%) demonstrated mononucleotide repeat instability, and the instability was at a single locus. We conclude that MSI, including mononucleotide repeat instability, is infrequent in human neuroblastoma, and therefore defects in DNA mismatch repair are not responsible for the genomic instability seen in this neoplasm.

Meningioma is a common tumor of the central nervous system. Deletions of the short arm of chromosome 1 (1p) are the second most commonly observed chromosomal abnormality in these tumors. Here, we analyzed tumor and normal DNAs from 157 meningioma patients using PCR-based polymorphic loci. Loss of heterozygosity (LOH) for at least one informative marker on 1p was observed in 54 cases (34%), whereas LOH on 1q occurred in only 9 cases (8%). High-resolution deletion mapping defined a consensus region of deletion flanked distally by D1S2713 and proximally by D1S2134, which spans 1.5 cM within 1p32. LOH in this region has also been observed in several other malignancies, suggesting the presence of a tumor suppressor gene or genes that are important for several types of cancer. Statistical analysis revealed that 1p LOH was associated with chromosome 22 deletions and with abnormalities of the NF2 gene in meningioma. In addition, unlike other clinical and molecular characteristics, only 1p LOH was shown to be significantly associated with recurrence-free survival.

Several human malignancies frequently exhibit deletions or rearrangements of the distal short arm of chromosome 1 (1p36), and a number of genetic diseases also map to this region. The carbonic anhydrase (CA6) and alpha-enolase (ENO1) genes, previously mapped to 1p36, were physically linked in yeast- and P1-artificial chromosome (YAC and PAC) contigs. PACs from the contig were mapped to 1p36.2 by fluorescence in situ hybridization. The ESTs D1S2068, D1S274E, D1S3275, and stSG4370 were also placed in the same contig. The physical map was integrated with the genetic map of chromosome 1 by assignment of genetic markers D1S160, D1S1615, and D1S503 to the contig. Sequencing of the EST clone representing D1S274E indicated that it was derived from the same transcript as D1S2068E and corresponded to the SLC2A5 (GLUT5) gene, previously assigned to 1p31. Reassignment of SLC2A5 to 1p36.2 was confirmed by somatic cell and radiation hybrid mapping panels and was consistent with previous EST mapping data. Sequencing of the EST clone for D1S274E revealed the presence of intronic sequences, suggesting that the clone was derived from an unprocessed message. The presence of unprocessed and/or alternatively spliced EST clones has potential ramifications for EST-based genomic projects. This information should facilitate the mapping of tumor suppressor and genetic disease loci that have been localized to this region.