High-resolution cytogenetic mapping of the short arm of chromosome 1 with newly isolated 411 cosmid markers by fluorescence in situ hybridization: the precise order of 18 markers on 1p36.1 on prophase chromosomes and "stretched" DNAs

Fluorescent in situ hybridization of DNA probes in the interphase and metaphase stages of the cell cycle

In the past decade, fluorescent in situ hybridization (FISH) has been used routinely in detecting molecular abnormalities in the interphase and metaphase stages of the cell cycle. Many of the molecular anomalies which are detected in this manner are diagnostic of a prenatal, postnatal, or neoplastic genetic disorder. With the continuous isolation of commercially available DNA probes specific to a particular chromosome region, FISH analysis has become standardized in its ability to detect characteristic chromosomal anomalies in association with genetic and neoplastic diseases. In recent years, FISH has also become automated to accommodate the increased volume of slide preparations necessary for the number of DNA probes needed to detect characteristic molecular anomalies in cancer tissues and bone marrow samples. FISH technology provides essential information to the physician regarding the diagnosis, response to treatment, and ultimately the prognosis of their patients' disorder. It has become an important source of information routinely used in conjunction with chromosome analyses, and presently to confirm molecular alterations detected by array comparative genomic hybridization (aCGH) analyses. In this chapter we describe the methods for performing FISH analyses in order to determine the presence or the absence of genetic abnormalities which define whether the patient has either a genetic syndrome or malignant disease.

Diagnostic clinical application of two-color fluorescence in situ hybridization that detects chromosome 1 and 17 alterations to direct touch smear and liquid-based thin-layer cytologic preparations of endometrial cancers

We performed two-color fluorescence in situ hybridization (FISH) on direct touch smears and liquid-based thin-layer (ThinPrep) cytological preparations of endometrial tumors to detect alterations of chromosome 1 and 17 that present with high incidence in endometrial cancers. The DNA probes used for two-color FISH analysis were a combination of the probes designed for 17cen (cCI 17-321) and 17p13.3 (D17S34), and a combination of the probes designed for 1q12 (D1Z1) and 1p36 (cCI1-5335). Numerical or structural alterations of chromosome 1 and/or 17 were detected in 95% (19 of 20 cases) of the direct touch smears obtained from endometrial cancer, while these alterations were also detected in 93% (12 of 13 cases) of samples obtained from grade 1 endometrioid adenocarcinoma cases, including three cases that could not be diagnosed as positive by conventional Papanicolaou cytopathologic staining. Using ThinPrep cytopathologic preparations, numerical or structural abnormalities were found in 26 (90%) and five (100%) cases, respectively, of samples obtained transcervically from 29 endometrial cancer and five atypical endometrial hyperplasia cases. Therefore, two-color FISH may be a useful diagnostic method for endometrial adenocarcinoma and premalignant lesions that demonstrate only slight cellular atypia in conventional cytopathologic preparations.

Correlation between genetic alteration and long-term clinical outcome of patients with oligodendroglial tumors, with identification of a consistent region of deletion on chromosome arm 1p

BACKGROUND

In oligodendroglial tumors, allelic losses on chromosome arms 1p and 19q are not only diagnostic molecular markers but also statistically significant predictors of both chemosensitivity and longer recurrence-free survival. In the current study, the authors attempted to analyze 21 patients genetically and clinically, with special emphasis on the correlation between genetic alterations and long-term therapeutic results.

METHODS

The authors reviewed the clinical cases of 21 patients who had undergone surgery for oligodendroglial tumors (13 oligodendrogliomas, World Health Organization [WHO] Grade II; 3 anaplastic oligodendrogliomas, WHO Grade III; 3 oligoastrocytomas, WHO Grade II; and 2 anaplastic oligoastrocytomas, WHO Grade III). Genetic testing for 1p deletions was performed using fluorescence in situ hybridization, and testing for 1p, 17p, and 19q deletions was carried out by microsatellite analysis. Survival was analyzed with univariate and multivariate Cox regression models. In addition, a high-resolution deletion map of 1p, which led to the discovery of a new deleted region on 1p, was obtained.

RESULTS

Statistical analysis revealed that both loss of 1p and loss of 19q independently and significantly predicted overall survival. A high-resolution deletion map, which displayed unusually narrow deletions, revealed a new region of deletion between D1S513 and D1S458 (1p34.3-36.11).

CONCLUSIONS

One of the putative tumor suppressor loci exists more proximally than ever reported. Based on the observation that 1p and 19q deletions predicted survival, the authors suggest further use of diagnostic and prognostic genetic testing in the clinical setting.

A consistent region of deletion on 1p36 in meningiomas: identification and relation to malignant progression

We analyzed the genetic aberrations on chromosome arms 1p, 10q, and 14q, which are thought to be loci that include putative tumor suppressor genes in meningiomas. We initially conducted molecular genetic testing on a total of 72 tumors including 15 atypical and 8 anaplastic meningiomas using double-target fluorescence in situ hybridization. An incidence of deletion of 1p was observed in 16.3% of histologically benign, 86.7% of atypical, and 87.5% of anaplastic meningiomas. Microsatellite analysis for loss of heterozygosity on 1p, 10q, and 14q was performed in 15 tumors (6 benign, 6 atypical, and 3 anaplastic meningiomas). We detected alimited deleted region on 1p36 in two tumors and suggest a new consistent region of deletion at 1p36.21 approximately p23 distal to D1S507 and proximal to D1S214, which spans 8.21 megabases. In addition, loss of 10q was detected in two of three secondary atypical meningiomas, and loss of 14q in two of three primary anaplastic meningiomas. We suggest that one of the putative suppressor genes is located at 1p36.21 approximately p23, and that 10q loss may contribute to the malignant progression from benign to atypical meningiomas.

The evolution and formation of RH genes

The Rh system clinically is one of the important blood groups. The major Rh antigens, which are constituted by over 40 types, are RhD, RhC/c, and RhE/e. Furthermore, Rh blood group system is characterized by the existence of many variants. It was considered that Rh blood group system was encoded on two genes termed the RHCE and RHD, which are composed of ten exons, respectively. It is inferred that the RHD gene encodes the RhD antigen and that the RHCE gene encodes the Rh C/c and RhE/e antigens. There are RHce, RHCe, RHcE and RHCE alleles as polymorphisms of RHCE gene. In 2000, the entire nucleotide sequences in all introns of both the RHD and RHCE genes were determined. Due to the new findings on RH genes, it is thought that multiple recombination (and/or gene conversion), nucleotide substitutions, small nucleotide gaps, replication slippage of microsatellite, large nucleotide gaps (due to Alu sequence) and the high level of the homology (%) between both RH genes are the important factors in the formation and evolution of both RH genes and Rh variants. Based on the advance of human genome project, the new interpretations on the evolution and formation of RH genes and Rh variants will be performed. Human Rh family (superfamily) and its counterparts in primates, mammals, fish, amphibians, bacteria, lower eukaryotes, archaea and plants have been identified. A lot of findings have been accumulated in their evolution and function. As gene conversions or recombination events confuse the phylogenetic tree of human RH genes and their counterparts, careful attention is necessary for researchers to calculate the time of gene duplication and to discuss the evolution of Rh family and its counterparts.Rh genotyping methods will never be perfect and both the clinicians and researchers have to recognize the limitation of Rh genotyping, especially RhD genotyping, because new Rh variants must have formed continually. In applying the Rh genotyping to clinical medicine, especially transfusion medicine, it is necessary to compare and examine the serological (phenotypic) data in Rh blood group system with caution.

A BAC-Based STS-Content Map Spanning a 35-Mb Region of Human Chromosome 1p35–p36

We have devised a mapping method for rapid assembly and ordering of bacterial artificial chromosome (BAC) clones on a radiation hybrid (RH) panel, using sequence-tagged sites (STSs) and PCR. The protocol consists of two rounds of two-dimensional screening from a limited number of BACs to correspond each to an STS. In the first round, STSs are assembled in the RH bins and ordered according to PCR signals derived from 384-well microtiter plates (MTPs) in which BAC clones have been arrayed. In the second round, individual BAC clones are isolated from the MTPs to build a contig. We applied this method to a 35-Mb region spanning human chromosome 1p35-p36 and assembled 1366 BACs in 11 contigs, the longest being about 20 Mb. The working draft sequences of the human genome have been integrated into the contigs to validate the accuracy.

An improved rapid procedure for fluorescence in situ hybridization that is applicable to intraoperative cancer cytodiagnosis

Fluorescence in situ hybridization (FISH) is among the most simple and useful methods for detecting numerical and structural aberration of chromosomes but it requires 12-24 h to complete. We devised a rapid FISH method that can be performed within 2 h. Here we describe the technique, which we have found to be extreme simple and as sensitive and specific as standard FISH, making it highly suitable for clinical use.

Gros1, a potential growth suppressor on chromosome 1: its identity to basement membrane-associated proteoglycan, leprecan

By immunoscreening with an antibody raised against a plasma membrane protein, we have cloned a growth suppressor gene, Gros1 and assigned it to short arm of human chromosome 1. Two alternatively spliced forms of the gene encoding 84- and 41-kDa (carboxy-terminus truncated) proteins were cloned. The two transcripts, 4.4 and 2.7 kb, were expressed weakly in most of the human tissues, with a high expression of the smaller transcript in placenta, ovary and testis. Normal human fibroblasts in culture showed two transcripts, with a higher level of expression of the 4.4 kb transcript. Transformed cells on the other hand showed predominant expression of the 2.7 kb transcript. Two Gros1 transcripts were also detected in most of the mouse tissues. Stable transfection of the mouse cDNA encoding the 85-kDa protein into NIH3T3 cells resulted in their slow growth and reduced colony-forming efficiency. Stable clones expressing antisense RNA on the other hand exhibited higher colony forming efficiency. While our data implied that Gros1 is a novel growth suppressor gene on human chromosome 1, an independent study has recently characterized its rat-homolog as a leucine proline-enriched novel basement membrane-associated proteoglycan leprecan. We describe here cloning, expression and biological activity analysis implying that this novel proteoglycan is a potential growth suppressor on chromosome 1p31, frequently altered in many malignancies.

Detailed deletion mapping of chromosome band 14q32 in human neuroblastoma defines a 1.1-Mb region of common allelic loss

Neuroblastoma (NB) is a well-known malignant disease in infants, but its molecular mechanisms have not yet been fully elucidated. To investigate the genetic contribution of abnormalities on the long arm of chromosome 14 (14q) in NB, we analysed loss of heterozygosity (LOH) in 54 primary NB samples using 12 microsatellite markers on 14q32. Seventeen (31%) of 54 tumours showed LOH at one or more of the markers analysed, and the smallest common region of allelic loss was identified between D14S62 and D14S987. This region was estimated to be 1-cM long from the linkage map. Fluorescence in situ hybridization also confirmed the loss. There was no statistical correlation between LOH and any clinicopathologic features, including age, stage, amplification of MYCN and ploidy. We further constructed a contig spanning the lost region using bacterial artificial chromosome and estimated this region to be approximately 1.1-Mb by pulsed-field gel electrophoresis. Our results will contribute to cloning and characterizing the putative tumour-associated gene(s) in 14q32 in NB.

Identification of a 700-kb region of common allelic loss in chromosome bands 3p14.3-p21.1 in human renal cell carcinoma

The short arm of chromosome 3 is considered to harbor one or more of the tumor suppressor genes taking part in the genesis of renal cell carcinoma (RCC). To define the localization of such putative tumor suppressor gene(s), we studied specific allelic loss on chromosome 3p by using 84 samples of RCC with nine microsatellite markers. We defined two commonly deleted regions in 3p14.3-p21.2: (1) region A, a 2-cM region between D3S1313 and D3S1592, and (2) region B, a 2-cM region between D3S1581 and D3S1289. The most frequent loss of heterozygosity was observed at D3S1067 (33 of 59, 55.9%), which is within region A. We further focused on region A and constructed a yeast artificial chromosome (YAC) contig and found that one YAC clone, which was 700-kb in size, harbored the entire region A. Using cosmid clones isolated from this contig, we also performed fluorescence in situ hybridization analysis and found that two of the tumors were homozygously deleted in this region. Our results strongly suggest the existence of a tumor suppressor gene in this region.

Ploidy analysis in paraffin-embedded malignant fibrous histiocytoma by DNA cytofluorometry and flourescence in situ hybridization

To prove the relationship between chromosomal aberration and DNA ploidy in human malignant fibrous histiocytoma (MFH), fluorescence in situ hybridization (FISH) and DNA cytofluorometry were performed in this study. For FISH study, the nucleus of each tumor cell was isolated from paraffin-embedded tissue of nine MFHs. Five chromosome-specific DNA probes (1p36, 1q12, 8q21.3, 11 centromere, and 17 centromere) were hybridized on cell nuclei. Cells with more than three probe signals were regarded as chromosome polysomy. All of the tumors analyzed by FISH had extra copies. The average percentage of polysomy in all tumors was high, ranging from 10.2% to 49.2%. The DNA ploidy patterns, and the percentage of hyperdiploid cells showing a greater DNA content than diploid cells, were obtained from DNA cytofluorometry. Three of nine were diploid patterns and six were non-diploid patterns, and the percentage of hyperdiploid cells in all tumors was high, ranging from 9.1% to 61.9%. The percentage of polysomy could be correlated with the percentage of hyperdiploid cells in each cell. In this study, we found that the DNA ploidy change was closely correlated with aberrations of chromosome copy number in MFH. In addition, the alterations of specific chromosome copy number could be detected in MFH showing diploid cells. Thus, these data indicate that FISH and DNA cytofluorometry are available as a cytogenetic tool for the analysis of interphase nuclei of bone and soft tissue tumors including MFH.

An integrated transcript map of human chromosome 1p35-p36

The distal short arm of human chromosome 1 (1p) is rearranged in a variety of malignancies, and several genetic diseases also map to this region. We have constructed an integrated transcript map to precisely define the positions of genes and expressed sequence tags (ESTs) previously mapped to 1p35-p36, a region spanning approximately 40 Mb. To anchor the integrated map, a framework genetic map was constructed with 24 genetic markers and a marker order of 1000:1 odds, yielding an average resolution of 2.8 cM. An additional 106 genetic markers were localized relative to the framework genetic map. To place markers more precisely within 1p35-p36, a chromosome 1-specific, radiation-reduced hybrid (RH) panel was created. Individual DNA fragments of the RH panel were identified and ordered by PCR with the framework genetic map. A total of 250 markers, including 142 genes and ESTs, were mapped by PCR against the RH panel. The map has an observed resolution of 800 kb, and the results closely match and more precisely define previous mapping information for most markers. This map will help to identify candidate genes for genetic diseases mapping to distal 1p and is fully integrated with existing genetic and RH maps of the human genome.

Genomic instability in 1p and human malignancies

Both cytogenetic and molecular genetic approaches have unveiled non-random genomic alterations in 1p associated with a number of human malignancies. These have been interpreted to suggest the existence of cancer-related genes in 1p. Earlier studies had employed chromosome analysis or used molecular probes mapped by in situ hybridization. Further, studies of the various tumor types often involved different molecular probes that had been mapped by different technical approaches, like linkage analysis, radioactive or fluorescence in situ hybridization, or by employing a panel of mouse x human radiation reduced somatic cell hybrids. The lack of maps fully integrating all loci has complicated the generation of a comparative and coherent picture of 1p damage in human malignancies even among different studies on the same tumor type. Only recently has the availability of genetically mapped, highly polymorphic loci at (CA)n repeats with sufficient linear density made it possible to scan genomic regions in different types of tumors readily by polymerase chain reaction (PCR) with a standard set of molecular probes. This paper aims at presenting an up-to-date picture of the association of 1p alterations with different human cancers and compiles the corresponding literature. From this it will emerge that the pattern of alterations in individual tumor types can be complex and that a stringent molecular and functional definition of the role that Ip alterations might have in tumorigenesis will require a more detailed analysis of the genomic regions involved.

Deletion of 1p36 in childhood endodermal sinus tumors by two-color fluorescence in situ hybridization: a pediatric oncology group study

Childhood endodermal sinus tumors (CESTs) are a unique category of germ cell tumors involving the testis and extragonadal region in children less than 4 years of age. Recent studies of CEST have shown recurrent cytogenetic abnormalities involving the short arm of chromosome 1, most commonly, a deletion of distal 1p. Experience with neuroblastomas has shown that cytogenetic analyses may underestimate the frequency of 1p deletion. To determine the frequency of deletion of Ip in CEST and to verify that 1p is, in fact, deleted and not translocated, we analyzed ten tumors by two-color fluorescence in situ hybridization on single-cell suspensions of interphase nuclei by using a cosmid probe from the PITSLRE kinase (p58) locus (previously mapped to 1p36) cohybridized with plasmid probe pUC1.77 (which recognizes the 1q heterochromatic region) to determine the copy number of chromosome 1. Eight of the ten tumors examined showed evidence of deletion of 1p36. Five of the eight tumors exhibited multiple subdones, and all subdones showed deletion of at least one copy of 1p36, indicating that the deletion probably occurred before the development of chromosome 1 aneusomy. We conclude that deletions of the short arm of chromosome 1, specifically 1p36, do occur in CEST and probably occur at a, higher incidence than that found in neuroblastoma Further studies are needed to determine the degree of overlap of the common area of deletion in CEST with that of neuroblastoma and to determine whether 1p deletion in CEST has prognostic significance.

The Japan Society of Human Genetics Award Lecture. Application of DNA markers to clinical genetics

DNA technology using DNA sequence polymorphisms has brought a new system to the fields of medicine and forensic science, especially for the studies of genetic diseases and tumor suppressor genes, and for identification of individuals for forensic purpose. Linkage analysis based on segregation of polymorphic alleles in affected families has contributed to identification of many genetic disease. We isolated a large number of polymorphic DNA markers, called VNTR (variable number of tandem repeat) markers and identified the APC gene that is responsible for familial adenomatous polyposis (FAP) by means of a so-called "positional cloning" and characterized germline and somatic mutations of the APC gene in colorectal cancer patients. In addition, we have applied genetic information during colorectal carcinogenesis to sensitive diagnosis of lymph-node metastasis of colorectal cancer.

Frequent deletions of material from chromosome arm 1p in oligodendroglial tumors revealed by double-target fluorescence in situ hybridization and microsatellite analysis

We undertook a cytogenetic analysis of 29 human brain tumors using double-target fluorescence in situ hybridization (FISH) and focusing on chromosome arm 1p. One or more tumor suppressor genes in this arm have been suggested to be important in a variety of neuroectodermal tumors. The series included 9 oligodendrogliomas, 4 mixed gliomas, 10 astrocytomas, 4 glioblastomas, and 2 central neurocytomas. We hybridized pericentromeric (1q12) and subtelomeric (1p36) DNA probes to cell nuclei prepared from paraffin-embedded tissues and observed a strikingly high incidence of deletion of at least part of 1p in oligodendrogliomas (100%) and mixed gliomas (75%). The results of the FISH analyses were confirmed by demonstration of loss of heterozygosity for a microsatellite polymorphism in 10 of the 29 tumors. As well as supporting the feasibility of FISH for detecting allelic deletions in chromosomes from paraffin-embedded tumor samples, the alteration of 1p reported here will contribute to an understanding of the molecular genetic events in oligodendroglial tumor development.

Structural organization and chromosomal assignment of the human obese gene

The obese (ob) gene has been identified through a positional cloning approach; the mutation of this gene causes marked hereditary obesity and diabetes mellitus in mice. We report here the isolation and characterization of the human ob gene. Southern blot analysis demonstrated a single copy of the ob gene in the human genome. The human ob gene spanned approximately 20 kilobases (kb) and contained three exons separated by two introns. The first intron, approximately 10.6 kb in size, occurred in the 5'-untranslated region, 29 base pair (bp) upstream of the ATG start codon. The second intron of 2.3 kb in size was located at glutamine +49. By rapid amplification of 5'-cDNA ends, the transcription initiation sites were mapped 54-57 bp upstream of the ATG start codon. The 172-bp 5'-flanking region of the human ob gene contained a TATA box-like sequence and several cis-acting regulatory elements (three copies of GC boxes, an AP-2-binding site, and a CCAAT/enhancer-binding protein-binding site). By the fluorescence in situ hybridization technique, the ob gene was assigned to human chromosome 7q31.3. This study should establish the genetic basis for ob gene research in humans, thereby leading to the better understanding of the molecular mechanisms underlying the ob gene.