Long range physical map of the Wilms' tumor-aniridia region on human chromosome 11

Characterization of Associated Nonclassical Phenotypes in Patients with Deletion in the WAGR Region Identified by Chromosomal Microarray: New Insights and Literature Review

WAGR syndrome (Wilms' tumor, aniridia, genitourinary changes, and intellectual disability) is a contiguous gene deletion syndrome characterized by the joint deletion of PAX6 and WT1 genes, located in the short arm of chromosome 11. However, most deletions include other genes, leading to multiple associated phenotypes. Therefore, understanding how genes deleted together can contribute to other clinical phenotypes is still considered a challenge. In order to establish genotype-phenotype correlation in patients with interstitial deletions of the short arm of chromosome 11, we selected 17 patients with deletions identified by chromosomal microarray analysis: 4 new subjects and 13 subjects previously described in the literature with detailed clinical data. Through the analysis of deleted regions and the phenotypic changes, it was possible to suggest the contribution of specific genes to several nonclassical phenotypes, contributing to the accuracy of clinical characterization of the syndrome and emphasizing the broad phenotypic spectrum found in the patients. This study reports the first patient with a PAX6 partial deletion who does not present any eye anomaly thus opening a new set of questions about the functional activity of PAX6.

Bilateral Wilms Tumor: A Surgical Perspective

Historically, the management of bilateral Wilms tumor (BWT) was non-standardized and suffered from instances of prolonged chemotherapy and inconsistent surgical management which resulted in suboptimal renal and oncologic outcomes. Because of the risk of end-stage renal disease associated with the management of BWT, neoadjuvant chemotherapy and nephron-sparing surgery have been adopted as the guiding management principles. This management strategy balances acceptable oncologic outcomes against the risk of end-stage renal disease. A recent multi-institutional Children’s Oncology Group study (AREN0534) has confirmed the benefits of standardized 3-drug neoadjuvant chemotherapy and the utilization of nephron-sparing surgery in BWT patients; however, less than 50% of patients underwent bilateral nephron-sparing surgery. The coordination of neoadjuvant chemotherapy and the timing and implementation of bilateral nephron-sparing surgery are features of BWT management that require collaboration between oncologists and surgeons. This review discusses the surgical management strategy in the context of BWT disease biology, with an emphasis on timepoints during therapy at which surgical decision making can greatly impact this disease and minimize long-term toxicities.

Characterization of an evolutionarily conserved metallophosphoesterase that is expressed in the fetal brain and associated with the WAGR syndrome

Among the human diseases that result from chromosomal aberrations, a de novo deletion in chromosome 11p13 is clinically associated with a syndrome characterized by Wilms' tumor, aniridia, genitourinary anomalies, and mental retardation (WAGR). Not all genes in the deleted region have been characterized biochemically or functionally. We have recently identified the first Class III cyclic nucleotide phosphodiesterase, Rv0805, from Mycobacterium tuberculosis, which biochemically and structurally belongs to the superfamily of metallophosphoesterases. We performed a large scale bioinformatic analysis to identify orthologs of the Rv0805 protein and identified many eukaryotic genes that included the human 239FB gene present in the region deleted in the WAGR syndrome. We report here the first detailed biochemical characterization of the rat 239FB protein and show that it possesses metallophosphodiesterase activity. Extensive mutational analysis identified residues that are involved in metal interaction at the binuclear metal center. Generation of a rat 239FB protein with a mutation corresponding to a single nucleotide polymorphism seen in human 239FB led to complete inactivation of the protein. A close ortholog of 239FB is found in adult tissues, and biochemical characterization of the 239AB protein demonstrated significant hydrolytic activity against 2',3'-cAMP, thus representing the first evidence for a Class III cyclic nucleotide phosphodiesterase in mammals. Highly conserved orthologs of the 239FB protein are found in Caenorhabditis elegans and Drosophila and, coupled with available evidence suggesting that 239FB is a tumor suppressor, indicate the important role this protein must play in diverse cellular events.

Pulsed-field gel electrophoresis for long-range restriction mapping

This unit describes procedures for generating long-range restriction maps of genomic DNA and for analysis of large insert clones. The basic protocol details restriction digestion of agarose-embedded DNA, PFGE separation, Southern transfer, and hybridization. Support protocols describe the preparation of high-molecular-weight genomic DNA samples in agarose blocks and in agarose microbeads, respectively. Additional support protocols describe the preparation of DNA size standards from l phage and two yeast species, Saccharomyces cerevisiae and Schizosaccharomyces pombe. An alternative method of preparing S. cerevisiae size standards using lithium dodecyl sulfate (LiDS) solubilization is provided. The final protocol details the preparation of BAC DNA suitable for digestion, mapping, and sequencing.

Missense mutations in the DNA-binding region and termination codon in PAX6

We have identified nine novel intragenic mutations of the PAX6 gene in 30 patients with aniridia. One patient with Wilms' tumor, aniridia, genitourinary anomalies, and mental retardation (WAGR syndrome) had deletion of 11p and had lost the paternal PAX6 allele. Two patients had small deletions: a frameshift that should result in early termination of the PAX6 protein, and a frameshift that leads to a termination-site change and run-on into the 3' untranslated region (UTR). The other 27 patients had single base-pair mutations. Four had splicing defects; three had IVS6+1G>A, which was at a mutation hotspot in the PAX6 gene; 10 had premature termination (four 1024C>T [R203X], also at a mutation hotspot); and six had missense mutations. Missense mutation A321T (1378G>A) was a polymorphic change; the other five missense mutations were L46R, C52R, I56T, G73D, and I87K. These five codons are in the PAX6 paired domain and are highly conserved throughout the entire paired family. Seven patients had a mutation in the normal stop codon (TAA). This change leads to run-on into the 3' UTR and is also at a mutation hotspot. All 30 mutations should result in PAX6 haploinsufficiency. No correlation was observed between mutation sites and phenotypes.

Screening for PAX6 gene mutations is consistent with haploinsufficiency as the main mechanism leading to various ocular defects

PAX6, a paired box transcriptional factor, is considered as the master control gene for morphogenesis of the eye. Human PAX6 mutations have been associated with a range of eye abnormalities, including aniridia, various anterior segment defects and foveal hypoplasia. We carried out a mutational analysis of the PAX6 gene in 54 unrelated patients with aniridia or related syndromes. A deleterious variation was evidenced in 17 sporadic cases (50%) and in 13 (72%) familial cases. Twenty-four different mutations, 17 of which are novel, were found. The spectrum of PAX6 mutations was highly homogeneous: 23 mutations (96%) leading to premature stop codons (eight nonsense and four splice site mutations, 11 insertions and deletions) and only one (4%) missense mutation. Twenty-two mutations were associated with aniridia phenotypes whereas two were associated with atypical phenotypes. These latter encompassed a missense mutation (R19P) in an individual with a microphthalmia-sclerocornea and a splice site mutation (IVS4+5G > C) in a family presenting with a congenital nystagmus. Both represented the most probably hypomorphic alleles. Aniridia cases were associated with nonsense or frameshifting mutations. A careful examination of the phenotypes did not make it possible to recognise significant differences whenever the predicted protein was deprived of one or another of its functional domains. This strongly suggested that most of the truncating mutations generated null alleles by nonsense mediated mRNA decay. Our observations support the concept of dosage effects of the PAX6 mutations as well as presenting evidence for variable expressivity.

Mutation in the PAX6 gene in twenty patients with aniridia

This is a report on the nature of the mutations in the PAX6 gene in twenty patients with aniridia. Five of the twenty patients had sporadic aniridia with deletions in chromosome 11p13. Three of the five had WAGR syndrome (Wilms tumor, aniridia, genitourinary anomalies, mental retardation), and the other two had deletions whose breakpoints occurred between the PAX6 and the WT1 genes. Allelic losses at PAX6 were of paternal origin. The remaining fifteen patients with aniridia had intragenic mutations in the PAX6 gene, with mutations found from exon 5 to exon 12. Twelve cases of dysfunctional PAX6 were due to premature termination of the protein by nonsense mutations (five cases), splicing defect (one case), deletion (two cases), deletion-insertions (two cases), and tandem repeat insertions (two cases). One patient (P2) had a PAX6 protein with de novo in-frame deletion of alanine, arginine, and proline at codon positions 37, 38, and 39. These codons are in the paired box region, and codon 38 is in contact with the phosphate group of the sugar-phosphate backbone of the target DNA. Another patient (P8) had a single nucleotide transition at c.1182 (nucleotide number, Genbank accession #M93650, used as in Glaser et al. [1992]), which generated both a missense mutation (Q255H) and a splicing defect. A missense mutation was found at G387E in a third patient (P10). All observed mutations support the notion that haploinsufficiency in PAX6 results in aniridia and associated eye anomalies.

Physical map of 17p13 and the genes adjacent to p53

Genetic lesions in the p53 tumor suppressor gene are the most frequently observed alterations in human cancers. Typically in tumors, one allele of the p53 gene is initially mutated, followed by deletion of the remaining wildtype allele. In human colon cancer, for example, approximately 70% of late stage tumors are hemizygous mutant p53. Since the precise gene environment surrounding the p53 gene is not known, the neighboring genes concomitantly lost with wildtype p53 deletion remain undetermined. A restriction enzyme map and clone array of 1.1 Mb surrounding the p53 gene were constructed using a combination of YAC, BAC, NotI linking, and NotI jumping clones. The resulting physical map and clone array include approximately 400 kb telomeric and 700 kb centromeric to the p53 gene. Sequence determination and analysis adjacent to NotI and AscI sites, indicative of CpG islands, allowed the rapid identification of numerous genes within the cloned region. Twenty-seven transcription units were identified, including 18 characterized genes. Limited analysis of primary human colon tumors, hemizygous for the p53 gene, indicates loss of the entire 1.1-Mb region upon deletion of wildtype p53.

A sequence-ready 3-Mb PAC contig covering 16 breakpoints of the Wilms tumor/anirida region of human chromosome 11p13

A large body of evidence that links alterations of chromosome 11p13 to tumor formation and various developmental disorders has been accumulated. To address the underlying genetic events it would be helpful to have a comprehensive gene map of the region, and this is most readily achieved by generating the complete genomic sequence. Building upon previous mapping and YAC contig analysis we have established a 3-Mb sequence-ready PAC contig. It was constructed by chromosome walking and independently verified by fingerprint analysis of individual clones. The contig starts from the catalase gene on the centromeric side and reaches beyond the PAX6 gene at the 11p13/p14.1 boundary. Additional smaller contigs on either side were identified, but still have to be linked up. The 3-Mb contig spans the central region of deletions encompassing 16 chromosomal breakpoints in patients with WAGR syndrome (Wilms tumor, aniridia, genitourinary malformation, mental retardation), and its construction is an important step in facilitating functional analysis of these genes.

Physical mapping of the mouse genome

This review is intended to provide an overview of techniques and a source of reagents for physical mapping of the mouse genome. It focuses on those applications, methods, or resources unique to the mouse and on the generation of comparative physical maps. The reference list is not comprehensive; rather, recent reviews on each topic and selected representative examples are given.

Transcription factor genes and the developing eye: a genetic perspective

We review the current knowledge of transcription factors in mammallan eye development. The 14 transcription factors presently known to be required for eye formation are examined in some detail, incorporating data from both humans and rodents. Aspects of the biochemistry, expression patterns, genetics, mutant phenotypes, and biological insights acquired from the examination of loss-of-function mutations are summarized. The other 32 tissue-restricted transcription factors that are currently known to be expressed in the developing or mature mammallan eye are tabulated, together with the timing and site of their ocular expression; the requirement for most of these genes in the eye is unknown. Contributions to mammallan eye development from the study of the genetics of the Drosophila eye are discussed briefly. Identification of the entire cohort of transcription factors required for eye development is an essential first step towards understanding the mechanisms underlying eye morphogenesis and differentiation, and the molecular basis of inherited eye abnormalities in humans.

Construction of a YAC contig encompassing the Usher syndrome type 1C and familial hyperinsulinism loci on chromosome 11p14-15.1

The Usher syndrome type 1C (USH1C) and familial hyperinsulinism (HI) loci have been assigned to chromosome 11p14-15.1, within the interval D11S419-D11S1310. We have constructed a yeast artificial chromosome (YAC) contig, extending from D11S926 to D11S899, which encompasses the critical regions for both USH1C and HI and spans an estimated genetic distance of approximately 4 cM. A minimal set of six YAC clones constitute the contig, with another 22 YACs confirming the order of sequence-tagged sites (STSs) and position of YACs on the contig. A total of 40 STSs, including 10 new STSs generated from YAC insert-end sequences and inter-Alu PCR products, were used to order the clones within the contig. This physical map provides a resource for identification of gene transcripts associated with USH1C, HI, and other genetic disorders that map to the D11S926-D11S899 interval.

Inheritance of unequal numbers of the genes encoding the human neutrophil defensins HP-1 and HP-3

It is unclear whether the six known human defensin peptides are all encoded by separate genes or whether some of them are allelic. Three of the peptides, HP-1, HP-2, and HP-3, differ by only one amino acid, and it is thought that HP-2 may represent a proteolytic product of HP-1 and/or HP-3. To help determine the relationship of these three proteins, we isolated a nearly full-length cDNA encoding HP-1 with a sequence very similar to, but different from, the previously isolated HP-1 and -3 cDNAs. Gene copy number experiments established that there were at least two but fewer than five defensin genes with a high level of similarity to the HP-1 cDNA (HP-1/3-like). Three genomic clones were isolated that contained two different configurations of the HP-1/3-like sequences. Sequencing established that one encoded the HP-1 peptide, whereas the other encoded HP-3. Analysis of DNAs obtained from 18 unrelated individuals by Southern blot analysis revealed the expected fragments as well as additional fragments that were not present in the genomic clones. This suggested the possibility of alleles; however, when DNAs from families were examined, these fragments did not segregate in an obvious Mendelian fashion. The HP-1/3-like defensin genes are on human chromosome 8. Surprisingly, somatic cell hybrid mapping showed that the number of HP-1/3-like genes on isolated copies of chromosome 8 was variable. We conclude that individuals can inherit versions of chromosome 8 harboring either two or three copies of the genes that encode the HP-1, HP-2, and/or HP-3 peptides.

Aniridia: recent achievements in paediatric practice

Aniridia is a rare panocular disorder which primarily involves not only the iris, but also the retina, optic nerve, lens and cornea. Visual acuity deteriorates as a result of nystagmus, glaucoma, cataract, corneal opacities and retinal hypoplasia. Aniridia may appear as an isolated disorder, most often familial with autosomal dominance or sporadically in association with at least 12 syndromes. Both familial isolated and Wilms tumour, bilateral sporadic aniridia, genitourinary abnormalities and mental retardation syndrome-associated aniridia have been traced to a mutation of the PAX6 gene on band 11p13. Since genetic diagnosis of this disorder is already possible, counselling affected families should be preceded by karyotype studies and linkage analysis in familial cases of isolated aniridia. In sporadic cases of isolated aniridia or WAGR syndrome, we suggest that PAX6 mutation analysis be employed.

CpG island clones for chromosome 11p--a resource for mapping and gene identification

A NotI end fragment library has been constructed for human Chromosome (Chr) 11p. Seventy-two clones were mapped to chromosomal subregions by use of somatic cell hybrids. The clones detect 44 different CpG islands, and we have isolated cosmid contigs for 36 of them. Extrapolation from the known 11p13 NotI restriction map suggests that every second CpG island from 11p containing a Not site is already represented in the clone collection. By sequence analysis all of the 11p13 clones exhibit typical features of CpG islands, and cross-species hybridization has been detected with at least one fragment in most cases. The cosmids serve as valuable linking clones for long-range restriction mapping. They also provide excellent starting material for transcript isolation procedures to identify genes on chromosome 11p associated with developmental anomalies and various tumor types. Several transcribed sequences have already been isolated with some of these clones.

A high-resolution integrated physical, cytogenetic, and genetic map of human chromosome 11: distal p13 to proximal p15.1

We describe a detailed physical map of human chromosome 11, extending from the distal part of p13 through the entirety of p14 to proximal p15.1. The primary level of mapping is based on chromosome breakpoints that divide the region into 20 intervals. At higher resolution YACs cover approximately 12 Mb of the region, and in many places overlapping cosmids are ordered in contiguous arrays. The map incorporates 18 known genes, including precise localization of the GTF2H1 gene encoding the 62-kDa subunit of TFIIH. We have also localized four expressed sequences of unknown function. The physical map incorporates genetic markers that allow relationships between physical and genetic distance to be examined, and similarly includes markers from a radiation hybrid map of 11. The cytogenetic location of cosmids has been examined on high-resolution banded chromosomes by fluorescence in situ hybridization, and FLpter values have been determined. The map therefore fully integrates physical, genic, genetic, and cytogenetic information and should provide a robust framework for the rapid and accurate assignment of new markers at a high level of resolution in this region of 11p.

Testicular germ cell tumors of adults show deletions of chromosomal bands 11p13 and 11p15.5, but no abnormalities within the zinc-finger regions and exons 2 and 6 of the Wilms' tumor 1 gene

We have studied the involvement of chromosomal bands 11p13 and 11p15.5 in 15 testicular seminomas (SE) and 18 testicular nonseminomatous germ cell tumors (NS). No allelic imbalances were found in 40% of the SE and 44% of the NS. Loss of heterozygosity (LOH) at 11p15.5 was seen in 21% of the SE and 47% of the NS; the corresponding frequencies for 11p13 were 47% and 44%. Both regions were deleted in 13% of the SE and 44% of the NS, indicating that all NS with a complete LOH of 11p13 also lost the 11p15.5 region. In one (out of two) SE and in five (out of eight) NS, this was due to at least two separate deletions. Loss of the whole p-arm was likely in one SE and two NS. No gross genomic changes of the Wilms' tumor 1 (WT1) tumor suppressor gene were found using a cDNA probe (WT33). Nor were aberrations found in the zinc-finger regions and exons 2 and 6 of this gene, using polymerase chain reaction amplification, single stranded DNA polymorphism analysis, and sequencing. We suggest that loss of genetic information from the short arm of chromosome 11, without affecting the WT1 gene in the regions studied, is relatively frequent but not crucial in the pathogenesis of testicular germ cell tumors of adults.

The molecular genetics of Wilms tumor: a paradigm of heterogeneity in tumor development

The evidence that genes on chromosome 11 are involved in Wilms tumor development is convincing; however, it is also evident that the mechanisms of tumorigenesis are more complex than the two-mutation model originally proposed. Potentially several genetic loci participate in Wilms tumor development. This should not be too surprising considering the complexity of pathways regulating growth and differentiation in nephrogenesis. It is possible that these various genes act at different points in the differentiation pathway and disruption of their normal function contributes to tumorigenesis. In fact, these loci may interact with one another in tumor formation. Certain types of genetic alterations may be the rate-limiting steps, but other changes may also contribute or be necessary for tumor development. Homozygous inactivation of specific genes, combinations of mutated alleles, and relaxation of genetic imprinting, or even interactions between different mutated alleles may all be part of the process for individual tumors. It has been found that some patients with the WAGR syndrome who are hemizygous for WT1 at 11p13 have in addition loss of heterozygosity within 11p15, and a sporadic tumor has been shown to have a WT1 mutation and loss of heterozygosity at loci at both 11p15 and 11p13 (59,85). These observations suggest the potential for interaction among the various Wilms tumor loci. Not only are there likely to be a number of different genetic loci linked to Wilms tumor development, but the mechanisms underlying altered gene function may be more variable than originally believed. It is probably not correct to think of Wilms tumor as a homogeneous entity. Mutations at different loci or various combinations of genetic lesions could well be responsible for the different categories of Wilms tumors. This apparent genetic complexity of Wilms tumor development is a concept that can very likely be applied to many other types of neoplasms. A complete understanding of Wilms tumorigenesis awaits identification of all members of the Wilms tumor gene family and the functional significance of their alterations.

Pax: gene regulators in the developing nervous system

In recent years, the discovery of Pax genes in mouse has played an invaluable role in furthering our understanding in mouse developmental processes and disorders. To date, eight murine paired box-containing genes have been cloned. Seven of these exhibit a distinct spatiotemporal expression pattern in the developing nervous system implying a role in the regional specification of the developing spinal cord and brain. The Pax genes encode for sequence-specific DNA binding transcription factors that play a key role in embryonic development. Three of these developmental control genes are altered in mutant mice and two are associated with human diseases. Disruption of these Pax genes leads to abnormalities in neural crest derivatives, neuroectoderm, sclerotome or myotome-derived tissues. Disruption of the Pax-3 gene causes the Splotch phenotype in mice and Waardenburg syndrome in humans. Pax-6 mutations result in Small eye mice and the human genetic disorder aniridia. The Pax-1 gene is mutated in undulated mice. Pax proteins can transform cells in culture which then form tumours following injection in nude mice. Consistent with this activity, PAX3 has been recently implicated in the generation of the tumour alveolar rhabdomyosarcoma.

Homozygous inactivation of WT1 in a Wilms' tumor associated with the WAGR syndrome

Wilms' tumor is a childhood nephroblastoma that is postulated to arise through the inactivation of a tumor suppressor gene by a two-hit mechanism. A candidate 11p13 Wilms' tumor gene, WT1, has been cloned and shown to encode a zinc finger protein. Patients with the WAGR syndrome (Wilm's tumor, aniridia, genitourinary abnormalities, and mental retardation) have a high risk of developing Wilms' tumor and they carry constitutional deletions of one chromosome 11 allele encompassing the WT1 gene. Analysis of the remaining WT1 allele in a Wilms' tumor from a WAGR patient revealed the deletion of a single nucleotide in exon 7. This mutation likely played a key role in tumor formation, as it prevents translation of the DNA-binding zinc finger domain that is essential for the function of the WT1 polypeptide as a transcriptional regulator.

Strategies for the molecular genetic analysis of obesity in humans

Studies of twins, adopted children, and some human populations indicate that body composition is significantly influenced by genetic factors. However, in no specific instance in either man or animals is the precise etiology of obesity known at the molecular level. Attempts to identify the molecular basis of obesity in humans have been hampered by difficulties in measuring food intake and energy expenditure with sufficient accuracy, as well as the apparent polygenic control of body composition in man. These constraints have stimulated interest in inbred animal strains, particularly mice, that have a genetic predisposition to obesity. Using the techniques of positional cloning, molecular markers flanking two autosomal recessive mouse obesity mutants (ob and db), which demonstrate a metabolic/behavioral phenotype similar to that observed in obese humans, have been identified. These markers are being used: (1) as starting points for chromosome walks to identify these genes, (2) as an aid in identifying genetically obese rodents prior to the development of the experimentally confounding obese phenotype, and (3) to investigate the possible contribution of the ob and db gene products to obesity in families segregating an obese phenotype. Additionally, genetic crosses segregating these obesity mutations are being used to identify "polygenes" that influence the severity of obesity and type II diabetes. Such studies may ultimately lead to the characterization of genes that influence the development and severity of obesity and non-insulin-dependent diabetes (NIDDM) in humans.

Molecular characterization of congenital mesoblastic nephroma and its distinction from Wilms tumor

BACKGROUND

Congenital mesoblastic nephroma (CMN) is a rare tumor of the neonatal kidney. It was once thought to be a variant of Wilms tumor that also arises from primitive renal cells.

METHODS

Molecular characteristics of two CMN were studied to clarify their potential relationship to Wilms tumors. Patterns of gene expression were assayed by Northern blot hybridization analysis. Tumors were tested for loss of heterozygosity (LOH) at chromosomes 11p13 and 11p15 using Southern blot analysis.

RESULTS

The CMN, like Wilms tumors, demonstrated high-level expression of insulin-like growth factor II. Unlike Wilms tumors, however, the CMN expressed neither the N-myc oncogene nor the putative Wilms tumor suppressor gene, WT1. Using a panel of probes spanning 11p13 and 11p15, no LOH was detected in the CMN, nor was there evidence of deletion or rearrangements of WT1.

CONCLUSIONS

Although Wilms tumor and CMN both arise from the developing kidney, molecular characterization suggests that different factors are involved in the pathogenesis of these two tumors.

Establishment of a highly sensitive and specific exon-trapping system

We have established a highly sensitive and specific exon-trapping system (SETS) with a specific plasmid vector in which an exon in a given DNA segment is identified by its ability to remain as a mature mRNA after splicing. The SETS provides us with the isolation of possible exons rapidly and easily from DNA fragments in chromosomal regions of more than 300 kilobase pairs. Genomic DNA fragments were partially digested and subsequently cloned into plasmid pMHC2, an exon-trapping vector we have constructed. These constructs were transfected into COS-7 cells, and consequent RNA transcripts were spliced in the cells. The resulting mature mRNA was harvested and amplified by using reverse transcription-PCR. Possible exons can be recognized by the sizes of PCR products and cloned into a plasmid vector. The SETS provides a direct means of cloning exons from genomic DNA of more than 300 kilobase pairs within a short period of time. Using this system, we have screened 300-kilobase-pair genomic DNA segments derived from human chromosome 11q13. Human chromosome 11q13 may contain genes responsible for human cancers, because DNA amplification is observed in several malignant tumors. We have successfully identified exon 2 of the HST1 gene and additional transcribed sequences.

Isolation of 1001 new markers from human chromosome 11, excluding the region of 11p13-p15.5, and their sublocalization by a new series of radiation-reduced somatic cell hybrids

The determination of the physical map of human chromosome 11 will require more clones than are currently available. We have isolated an additional 1001 new markers in a bacteriophage vector from a somatic cell hybrid cell line that contains most of chromosome 11, except the middle of the short arm. These markers were localized to five different regions, 11p15-pter, 11p12-cen, 11q11-q14, 11q14-q23, and 11q23-qter, by a panel of previously characterized somatic cell hybrids. The region 11q11-14 harbors genes that have been shown to be important in breast cancer, B-cell lymphomas, centrocytic lymphomas, asthma, and multiple endocrine neoplasia, type 1 (MEN1). To determine the positions of the recombinant clones located there, we developed a new series of radiation-reduced somatic cell hybrids. These hybrids, together with those previously characterized, allowed us to map the 11q11-q14 markers into 11 separate segregation groups.

The human BDNF gene maps between FSHB and HVBS1 at the boundary of 11p13-p14

To map in detail the human gene for brain derived neurotrophic factor (BDNF) we have used a PCR-based assay to amplify the gene from somatic cell hybrids containing human chromosome 11 with deletion or translocation breakpoints in the WAGR region. The BDNF gene maps between the FSHB and HVBS1 loci, an interval of approximately 4 Mb at the boundary of 11p13 and 11p14.

Resolution of the two loci for autosomal dominant aniridia, AN1 and AN2, to a single locus on chromosome 11p13

Two distinct loci have been proposed for aniridia; AN1 for autosomal dominant aniridia on chromosome 2p and AN2 for the aniridia in the WAGR contiguous gene syndrome on chromosome 11p13. In this report, the kindred segregating for autosomal dominant aniridia, which suggested linkage to acid phosphatase-1 (ACP1) and led to the assignment of the AN1 locus on chromosome 2p, has been updated and expanded. Linkage analysis between the aniridia phenotype and ACP1 does not support the original linkage results, excluding linkage up to theta = 0.17 with Z = -2. Tests for linkage to other chromosome 2p markers. APOB, D2S71, D2S5, and D2S1, also excluded linkage to aniridia. Markers that have been isolated from the chromosome 11p13 region were then analyzed in this aniridia family. Two RFLPs at the D11S323 locus give significant evidence for linkage. The PvuII polymorphism detected by probe p5S1.6 detects no recombinants, with a maximum lod score of Z = 6.97 at theta = 0.00. The HaeIII polymorphism detected by the probe p5BE1.2 gives a maximum lod score of Z = 2.57 at theta = 0.00. Locus D11S325 gives a lod score of Z = 1.53 at theta = 0.00. These data suggest that a locus for aniridia (AN1) on chromosome 2p has been misassigned and that this autosomal dominant aniridia family is segregating for an aniridia mutation linked to markers in the 11p13 region.

Small eye (Sey): cloning and characterization of the murine homolog of the human aniridia gene

Phenotypic parallels and genetic evidence from comparative mapping suggest that the murine Small eye (Sey) and human aniridia (AN) disorders are homologous. This report describes the isolation of a murine embryonic cDNA that is structurally homologous to the AN cDNA were recently cloned. The murine cDNA detects a 2.7-kb transcript in the adult mouse eye and cerebellum and in human glioblastomas, suggesting a neuroectodermal involvement in the etiology of Sey/AN. Sequence comparison between the murine and the human cDNAs revealed extensive homology in nucleotide sequence (greater than 92%) and virtual identity at the amino acid level. None of the differing amino acids was located within the paired box and homeobox DNA-binding domains. These results provide evidence for a common molecular basis underlying the two genetic disorders and suggest that the Sey system would be an authentic model for human AN.

Choice of enzymes for mapping based on CpG islands in the human genome

The frequencies of sites for rare-cutting restriction enzymes in 2.9 million bp of human genomic DNA sequence in the EMBL database have been determined and compared with the expected frequencies. Rare cutters can be divided into four groups based on certain features of their recognition sites. Mlu, I, Nru I, Spl I, and Pvu I are predicted to cleave genomic DNA most infrequently, which is borne out by the fragment lengths observed for Mlu I and Nru I. Thus, these four enzymes are ideal for making long-range maps based on pulsed-field electrophoresis. Other enzymes like Not I are useful for making more detailed maps. Finer maps for identification of CpG islands and associated genes should involve several rare cutters including Eag I, Sac II and Bss HII. A cluster of sites for at least two such enzymes is a good indicator of a CpG island, and 78% of the island-associated genes can be located in this way.

Wilms' tumour: reconciling genetics and biology

Wilms' tumour, a paediatric malignancy of the kidney, is a striking example of the relationship between aberrant development and cancer. Several different genetic loci have been implicated in the aetiology of the tumour; genomic imprinting also plays a role. One Wilms' tumour predisposition gene (WT1), encoding a zinc finger protein, is expressed in a limited set of tissues, including developing nephrons and gonads. The biology and genetics of Wilms' tumour underline the developmental relationship between kidneys and gonads.

The molecular biology of urological tumors

This article reviews the present understanding of chromosomal aberrations and specific genetic mutations in renal, bladder, and prostate cancers. In kidney tumors, specific emphasis is given to chromosome 3 deletions in renal cell carcinoma and the characterization of the WT1 gene in Wilms' tumor. In all three urological tumors, the presence of mutations in the RAS, P53, and RB genes (all of which often occur in other tumors) is analyzed. The expression and properties of the androgen receptor in prostate cancer are also summarized.

Positional cloning and characterization of a paired box- and homeobox-containing gene from the aniridia region

Based on the map location of the aniridia (AN) locus in human chromosomal band 11p13, we have cloned a candidate AN cDNA (D11S812E) that is completely or partially deleted in two patients with AN. The less than 70 kb smallest region of overlap between the two deletions encompasses the 3' coding region of the cDNA. This cDNA, which spans over 50 kb of genomic DNA, detects a 2.7 kb message specifically within all tissues affected in AN. The predicted polypeptide product possesses a paired domain, a homeodomain, and a serine/threonine-rich carboxy-terminal domain, structural motifs characteristic of certain transcription factors. The concordance between expression and pathology, map location, structure, and predicted function argues that the cDNA corresponds to the AN gene.

Physical mapping of the loci Gabra3, DXPas8, CamL1, and Rsvp in a region of the mouse X chromosome homologous to human Xq28

Using pulsed-field gel electrophoresis, a 3 million-bp physical map containing the X-linked loci Gabra3, DXPas8, CamL1, and Rsvp has been constructed for a segment of the mouse X chromosome homologous to human Xq28. Detailed mapping was performed using single and double digestions with rare-cutter restriction enzymes. Gabra3 and DXPas8 have been shown to be physically linked within a maximal distance of 1600 kb, DXPas8 and CamL1 within 750 kb, and CamL1 and Rsvp within 450 kb. In addition, several CpG islands have been detected in the region encompassing CamL1 and Rsvp. These studies confirm a gene order of cen-Gabra3-DXPas8-CamL1-Rsvp-tel determined by genetic mapping in interspecific backcrosses (A.S. Ryder-Cook et al., 1988, EMBO J. 7: 3017-3021; G.E. Herman et al., 1991, Genomics 9: 670-677). Physical distances for the loci studied agree with the calculated genetic distances. Assuming that there is conserved linkage between man and mouse in the region, the physical mapping data presented here may help to clarify the uncertain gene order for some human Xq28 loci.

Molecular genetic linkage maps of mouse chromosomes 4 and 6

We have generated a moderate resolution genetic map of mouse chromosomes 4 and 6 utilizing a (C57BL/6J x Mus spretus) F1 x Mus spretus backcross with RFLPs for 31 probes. The map for chromosome 4 covers 77 cM and details a large region of homology to human chromosome 1p. The map establishes the breakpoints in the mouse 4-human 1p region of homology to a 2-cM interval between Ifa and Jun in mouse and to the interval between JUN and ACADM in human. The map for mouse chromosome 6 spans a 65-cM region and contains a large region of homology to human 7q. These maps also provide chromosomal assignment and order for a number of previously unmapped probes. The maps should allow the rapid regional assignment of new markers to mouse chromosomes 4 and 6. In addition, knowledge of the gene order in mouse may prove useful in determining the gene order of the homologous regions in human.

A tumor chromosome rearrangement further defines the 11p13 Wilms tumor locus

A sporadic Wilms tumor, WT-21, with an (11;14)-(p13;q23) reciprocal translocation has been identified. The translocation is found in tumor cells, but not in the patients' circulating lymphocytes. Molecular analysis of somatic cell hybrids segregating the derivative translocation chromosomes reveals a submicroscopic interstitial deletion at the translocation breakpoint, as well as a cytologically undetectable interstitial deletion in the nontranslocation chromosome 11, resulting in a homozygous deletion in 11p13. Pulsed-field gel analysis of tumor DNA indicates that the two deletions are indistinguishable, and the homozygously deleted region is less than 875 kb. The homozygously deleted regions of three other sporadic Wilms tumors overlap with the deleted region in WT-21, and the candidate cDNA clone for the 11p13 Wilms tumor gene described by Call et al. (Cell 60, 509-520, 1990) is included in the deleted region. These findings strengthen previous conclusions regarding the obligate location for the 11p13 WT locus and support the suggestion that the Wilms tumor gene has been cloned.

Smallest region of overlap in Wilms tumor deletions uniquely implicates an 11p13 zinc finger gene as the disease locus

The development of Wilms tumor (WT) has been associated with the inactivation of a "tumor suppressor" locus in human chromosome 11 band p13. Several WTs that exhibit homozygous deletions of an 11p13 candidate WT gene in its entirety have been reported. We report here a partial deletion of the candidate gene which, upon comparison with other documented homozygous deletions, permitted a precise definition of the critical genomic target in Wilms tumor. The smallest region of overlap between these deletions is a 16-kb segment of DNA encompassing the 5' exon(s) of an 11p13 gene coding for a zinc finger protein, together with an associated CpG island. This finding supports the notion that the candidate gene in question corresponds to the 11p13 WT1 Wilms tumor locus.

PCR detection of a BglII RFLP at 11p13

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Direct pulsed field gel electrophoresis of Wilms' tumors shows that DNA deletions in 11p13 are rare

In order to search for small tumor-specific deletions in 11p13 we analysed DNA isolated from 30 fresh Wilms' tumor (WT) samples with pulsed field gel electrophoresis. For these studies we have isolated new probes from the ends of several Notl fragments. Using these and previously described probes from 11p13 we first completed and extended the existing map of the 11p13 region. The analysis of the tumor material showed that (I) tumor-specific deletions were very rare: one homozygous deletion out of 30 tumors analysed, (2) hemizygous deletions were not observed in any of the tumors. The homozygous deletion in one patient spans 220 kb and is composed of a tumor-specific translocation associated with a deletion on one chromosome and a deletion of about 220 kb on the other chromosome at the same site. The WT-33 Wilms' tumor candidate gene maps to this deleted segment. A small constitutional deletion of 1,300 kb was identified in a patient with WT and genital tract malformations. These results suggest that in the majority of sporadic WT loss of gene function is due to subtle alterations in the gene, e.g., point mutations or very small deletions.

Probes for CpG islands on the distal long arm of the human X chromosome are clustered in Xq24 and Xq28

We have isolated and characterized 55 EagI-containing genomic DNA clones from the distal long arm of the human X chromosome. The presence of additional sites for rare-cutter restriction enzymes and the demethylation of the corresponding genomic DNA demonstrate that at least 30 clones correspond to CpG islands of the Xq24-Xqter region. All clones were regionally mapped with a hybrid panel. The majority are in Xq28 and Xq24 (18 and 14 clones, respectively), 15 are in the Xq26-Xq27 interval, and none is in Xq25. This analysis demonstrates a nonuniform distribution of CpG islands that may reflect the distribution of coding regions in this part of the genome.

A mouse model of the aniridia-Wilms tumor deletion syndrome

Deletion of chromosome 11p13 in humans produces the WAGR syndrome, consisting of aniridia (an absence or malformation of the iris), Wilms tumor (nephroblastoma), genitourinary malformations, and mental retardation. An interspecies backcross between Mus musculus/domesticus and Mus spretus was made in order to map the homologous chromosomal region in the mouse genome and to define an animal model of this syndrome. Nine evolutionarily conserved DNA clones from proximal human 11p were localized on mouse chromosome 2 near Small-eyes (Sey), a semidominant mutation that is phenotypically similar to aniridia. Analysis of Dickie's Small-eye (SeyDey), a poorly viable allele that has pleiotropic effects, revealed the deletion of three clones, f3, f8, and k13, which encompass the aniridia (AN2) and Wilms tumor susceptibility genes in man. Unlike their human counterparts, SeyDey/+ mice do not develop nephroblastomas. These findings suggest that the Small-eye defect is genetically equivalent to human aniridia, but that loss of the murine homolog of the Wilms tumor gene is not sufficient for tumor initiation. A comparison among Sey alleles suggests that the AN2 gene product is required for induction of the lens and nasal placodes.