A transcript map encompassing the multiple endocrine neoplasia type-1 (MEN1) locus on chromosome 11q13

Genetics of type 1 diabetes mellitus

At least 20 different chromosomal regions have been linked to type 1 diabetes (T1D) susceptibility in humans, using genome screening, candidate gene testing, and studies of human homologues of mouse susceptibility genes. The largest contribution from a single locus (IDDM1) comes from several genes located in the MHC complex on chromosome 6p21.3, accounting for at least 40% of the familial aggregation of this disease. Approximately 30% of T1D patients are heterozygous for HLA-DQA1*0501-DQB1*0201/DQA1*0301-DQB1*0302 alleles (formerly referred to as HLA-DR3/4 and for simplification usually shortened to HLA-DQ2/DQ8), and a particular HLA-DQ6 molecule (HLA-DQA1*0102-DQB1*0602) is associated with dominant protection from the disease. There is evidence that certain residues important for structure and function of both HLA-DQ and DR peptide-binding pockets determine disease susceptibility and resistance. Independent confirmation of the IDDM2 locus on chromosome 11p15.5 has been achieved in both case-control and family-based studies, whereas associations with the other potential IDDM loci have not always been replicated. Several possibilities to explain these variable results from different studies are discussed, and a key factor affecting both linkage and association studies is that the genetic basis of T1D susceptibility may differ between ethnic groups. Some future strategies to address these problems are proposed. These include increasing the sample size in homogenous ethnic groups, high throughput genotyping and genomewide linkage disequilibrium (LD) mapping to establish disease associated ancestral haplotypes. Elucidation of the function of particular genes ('functional genomics') in the pathogenesis of T1D will be a most important element in future studies in this field, in addition to more sophisticated methods of statistical analyses.

Losses of heterozygosity in endometrial adenocarcinomas: positive correlations with histopathological parameters

We analyzed 37 samples of endometrial adenocarcinoma for loss of heterozygosity (LOH) by using a panel of 44 microsatellites located in 29 chromosomal regions. The aim of our study was to investigate the existence of a possible preferential involvement of some tumor suppressor genes in endometrial carcinogenesis. The analysis was performed on tumoral tissue and on a corresponding normal tissue by the use of polymerase chain reaction (PCR) and the comparison of the amplified alleles. We observed significative LOH (>20%) in the chromosomal regions of 2q14 (33.33%), 7q35 (24.00%), 10q22.1 (37. 50%), 11q13-q14 (44.12%), 15q26 (40.63%), 17p13 (25.71%), and 17q21. 3 (37.04%). We defined a 1-cM minimal common deletion in 11q13-q14 between D11S911 and D11S937 markers. A statistical analysis revealed a positive correlation between LOH of 11q13-q14 and clinicopathological data.

Construction of a 350-kb sequence-ready 11q13 cosmid contig encompassing the markers D11S4933 and D11S546: mapping of 11 genes and 3 tumor-associated translocation breakpoints

Previously, we located three novel human tumor-associated translocation breakpoints in the chromosome 11q13 region between the markers D11S4933 and D11S546. To facilitate the molecular analysis of these breakpoints, we have constructed a continuous sequence-ready cosmid and PAC contig of approximately 350 kb, including the markers D11S4933 and D11S546. In addition, a detailed transcript map was generated. This resulted in the precise positioning of 11 genes and ESTs within the contig, including 4 genes already known to map in the 11q13 region. Three other genes that we positioned within the contig showed homologies to unmapped genes from human and/or other species. Three ESTs were novel. Partial cosmid sequencing resulted in the establishment of the direction of transcription of several of the reported genes. This contig will be instrumental for the detailed characterization of the tumor-associated chromosomal breakpoints and the identification of other 11q13-associated disease genes.

A 2-Mb sequence-ready contig map and a novel immunoglobulin superfamily gene IGSF4 in the LOH region of chromosome 11q23.2

Human chromosome 11q23.2 has been proposed to contain a tumor suppressor gene(s) whose deletion has been associated with cancer of the lung and breast and with neuroblastoma. To analyze the genomic structure and to isolate a candidate tumor suppressor gene from this region, we constructed a 2-Mb sequence-ready contig map using bacteriophage P1 (P1), bacterial artificial chromosome (BAC), and P1-derived artificial chromosome (PAC). The map comprises a contig of 24 overlapping P1, BAC, and PAC clones. To isolate gene fragments from the region, we performed direct cDNA library screening, exon trapping, EST mapping, and genomic sequencing using the P1, BAC, and PAC clones. Sequence analysis of 5 clones, which spans 23% (458,738 bp) of the region, and extensive gene scanning along the entire region revealed that the region is extraordinarily scarce in genes, but we identified one ubiquitously expressed novel gene and one testis-specific gene fragment. The novel gene, which we call IGSF4 (immunoglobulin superfamily 4), is transcribed into a 1.6- or 4.4-kb RNA encoding a 442-amino-acid protein. It shares strong homology with mouse IGSF-B12 and cell adhesion molecules NCAM1 and NCAM2 within their Ig-like C2-type domains. The IGSF4 gene, a novel gene that is shown to be located in the common loss of heterozygosity region, possesses a number of interesting features and may be good candidate for a tumor suppressor gene.

A 500-kb sequence-ready cosmid contig and transcript map of the MEN1 region on 11q13

We have generated a transcript map of an approximately 1.2-Mb region from human chromosome band 11q13 between the loci VEGFB and CAPN1, which flank the multiple endocrine neoplasia type 1 (MEN 1) locus. In total, we isolated 144 cosmids from this region and generated a sequence-ready cosmid contig of the approximately 500-kb region between the neurexin locus and D11S2196E. We identified 54 genes/ESTs by sample sequencing and have constructed a transcript map of this region. Genes were found to be clustered in three regions, and one of these genes was identical to the recently identified MEN1 locus. Relative to the latter, we have mapped the positions of 13 known genes, 18 genes which show homology to genes from humans or other organisms, and 22 genes/ESTs that appear novel. In addition, we have ascertained the directions of transcription of some of these genes and have determined intergenic distances between many loci. Full characterization of some of these genes, as well as the novel ESTs, will be useful in identifying candidate genes for other diseases known to map to this chromosomal region.

Genomic organization and cloning of the human homologue of murine Sipa-1

Murine Sipa-1 (signal-induced proliferation associated protein) is a mitogen induced GTPase activating protein (GAP). While mapping candidate genes for multiple endocrine neoplasia type 1 (MEN1) at 11q13, we cloned the human homologue of Sipa-1. Herein, we report the complete cDNA sequence, expression, and genomic organization of SIPA-1. SIPA-1 consists of 16 exons with highly conserved exon-intron boundaries. The predicted SIPA-1 protein is highly homologous to the mouse protein, particularly in the region of the GAP-related domain at the amino terminus and the leucine zipper at the carboxy terminus. It is widely expressed, including in fetal tissues, but is most highly expressed in lymphoid organs. During the course of cloning SIPA-1, the MEN1 gene was identified, thus excluding human SIPA-1 as a candidate for this disease.

Deletion mapping of endocrine tumors localizes a second tumor suppressor gene on chromosome band 11q13

Multiple endocrine neoplasia type 1 syndrome (MEN1, MIM 131100), an autosomal dominant disease, is characterized by parathyroid hyperplasia, pancreatic endocrine tumors, and pituitary adenomas. These tumors also occur sporadically. Both the familial (MEN1) and the sporadic tumors reveal loss of heterozygosity (LOH) for chromosome band 11q13 sequences. Based on prior linkage and LOH analyses, the MEN1 gene was localized between PYGM and D11S460. Recently, the MEN1 gene (menin) has been cloned from sequences 30-kb distal to PYGM. We performed deletion mapping on 25 endocrine tumors (5 MEN1 and 20 sporadic) by using 21 polymorphic markers on chromosome band 11q13. Of these, two (137C7A, 137C7B) were derived from PYGM-containing BAC (bacterial artificial chromosome-137C7) sequences, one from INT2-containing cosmid sequences and the marker D11S4748, a (CA)20 repeat marker that was developed by us. The LOH analysis shows that the markers close to the MEN1 (menin) gene were not deleted in three of the tumors. These tumors, however, showed LOH for distal markers. Thus, the data suggest the existence of a second tumor suppressor gene on chromosome band 11q13.