Genome analysis and the human X chromosome

Monoclonal expansion with integration of high-risk type human papillomaviruses is an initial step for cervical carcinogenesis: association of clonal status and human papillomavirus infection with clinical outcome in cervical intraepithelial neoplasia

To define the natural history of cervical intraepithelial neoplasia (CIN) as related to clonal status, we evaluated 20 cases of CIN1 and 18 cases of CIN2 that had been clinically followed for 7 to 48 months at Osaka University Hospital. These included 10 cases that progressed, 15 cases that persisted, and 13 cases that regressed. We analyzed the clonal status of each case by analysis of the pattern of X-chromosomal inactivation. Human papillomavirus (HPV) infection was detected by PCR-RFLP analysis. CINs that are monoclonal or infected by high-risk HPVs are more likely to progress or persist than cases that are polyclonal or negative for high-risk HPVs (p = 0.009 for monoclonal vs polyclonal, p = 0.024 for high-risk HPV positive vs negative p = 0.024). Eighteen (90%) of 20 monoclonal, high-risk HPV-associated CINs progressed or persisted, whereas 9 (60%) of 15 polyclonal or high-risk HPV-negative CINs regressed. Therefore, the combination of clonality status and high-risk type HPV infection was significantly correlated with clinical outcome (p = 0.003). The physical status of the HPV genome was evaluated in 17 cases of HPV-16 positive CINs by real-time PCR. Of those, the HPV viral genome was present in both episomal and integrated forms in 14 CINs (84%), and 12 of these cases (86%) were monoclonal in composition. By contrast, all three CINs in which the HPV genome was present in episomal form were polyclonal. In one CIN1 that was polyclonal, HPV-16 was originally present in episomal form but after 24 months, the patient developed a monoclonal CIN3 in which the HPV-16 genome was present in mixed form. These results may imply that HPV viral integration into the host genomic DNA is associated with progression from polyclonal to monoclonal status in CIN. These events may play a fundamental role in the progression from low-grade to higher grade dysplasia of the cervical mucosa.

Clonal analysis and mutations in the PTEN and the K-ras genes in endometrial hyperplasia

The patterns of X chromosome inactivation and mutations of PTEN and K-ras were evaluated in cases of endometrial hyperplasia to determine the presence of potentially premalignant neoplastic versus polyclonal benign cell populations. Endometrial glandular epithelial cells were collected by laser capture microdissection, and genomic DNAs were extracted. Following treatment with the methylation sensitive restriction endonuclease Hha I, polymerase chain reaction amplification was performed targeting a highly polymorphic short tandem repeat of the human androgen receptor gene (HUMARA). PTEN and K-ras gene mutations were evaluated by analysis of single-strand conformation polymorphism. Two pathologists performed histologic diagnosis of the lesions independently. Monoclonal composition was demonstrated in 13 of 15 (87%) endometrial hyperplasias with atypia and 17 of 31 (55%) complex hyperplasias without atypia. Cytological atypia is significantly associated with the clonal status of the endometrial hyperplasia (13/15 vs 17/31, P = 0.049). In contrast, all 14 normal endometrial tissue samples were polyclonal. PTEN gene mutations were detected in 4 of 13 (30%) monoclonal endometrial hyperplasias with atypia and 2 of 17 (12%) monoclonal endometrial hyperplasias without atypia but were not detected in polyclonal endometrial hyperplasias, with or without atypia. K-ras gene mutations were present in 3 of 13 (23%) monoclonal endometrial hyperplasias with atypia but not in 2 cases of polyclonal endometrial hyperplasia with atypia or in 26 cases of endometrial hyperplasia without atypia. K-ras mutation is thus significantly more frequently found in endometrial hyperplasias with atypia than those without atypia (3/15 vs 0/31, P = 0.030). This study indicates that most cases of endometrial hyperplasia with atypia and a high proportion of cases of endometrial hyperplasias without atypia originate from a single progenitor cell, possibly as a result of genetic alterations, rather than as a result of benign reactive processes.

Differential expression of XAP5, a candidate disease gene

We have isolated a full-length cDNA corresponding to the XAP5 gene in Xq28. An unusual feature of the cDNA is that it contains runs of CCG repeats in the 5' untranslated region, typical of genes that exhibit anticipation. It has a striking pattern of differential expression and is greatly enhanced in various fetal tissues. This predicted protein encodes a unique 339-amino-acid polypeptide that contains a large percentage of highly charged residues and a possible nuclear localization signal. A comparison to genomic sequence shows that XAP-5 comprises 13 exons spanning 6.5 kb. An examination of the human population indicates that the longest CCG run is polymorphic and varies in length from 8 to 12 repeats.

Chromosomal mapping of five highly conserved murine homologues of the Drosophila RING finger gene seven-in-absentia

Seven-in-absentia (sina) is epistatic to all other known genes in the sevenless-ras signaling pathway, which mediates R7 photoreceptor formation in the Drosophila eye. The murine genome contains several closely related sina homologues (Siah1A-D, Siah2) that are also likely to participate in ras signaling. As part of a genetic and biochemical analysis of the mammalian Siah genes, we have used gene-specific probes to map the chromosomal positions of each family member. Here we report their chromosomal positions in relation to a number of known mouse mutations and also describe an analysis of the human Siah genes. By comparing the complexity of the Siah genes in these two mammalian species we have gained further insight into which members of this murine multigene family are likely to be functional.

Clonality analysis in tumours of women by PCR amplification of X-linked genes

Modifications have been made to two polymerase chain reaction (PCR) methods for clonality analysis based on the inactivation patterns of two highly polymorphic X-linked genes encoding the androgen receptor (AR) and monoamine oxidase A (MAOA). These methods have been used to examine the clonal nature of frozen tissues from 42 tumours and 25 non-tumour controls from female subjects. Unbalanced inactivation patterns of the genes, which indicate monoclonality, were frequently observed in tumours of heterozygous (informative) cases (18/35 = 51.4 per cent for the AR gene, 9/30 = 30 per cent for the MAOA gene, and 21/38 = 55.2 per cent for both). Among 23 informative non-tumour controls, only one (4.3 per cent), a reactive lymph node, showed skewing in the AR gene. Successful detection of monoclonality was found to depend on the proportion of tumour cells in the tissues examined. None of the AR or MAOA informative cases containing less than 50 per cent of tumour cells showed imbalance in inactivation patterns. With more than 50 per cent of tumour cells in the samples, 66.6 per cent (18/27) of AR and 39.1 per cent (9/23) of MAOA informative cases showed allelic imbalance, with a combined frequency of 72.4 per cent (21/29) of both genes. Our results demonstrate that the methods described are useful for clonal analysis of tissue samples from female patients.

4.5-Mb YAC STS contig at 50-kb resolution, spanning Xq25 deletions in two patients with lymphoproliferative syndrome

Sequence-tagged site (STS) content mapping in yeast artificial chromosomes (YACs) was used to cover the region deleted in two patients affected with X-linked lymphoproliferative disorder. The order of markers includes, centromere to telomere, DXS8009-DXS1206-DXS8078-DXS8044-DXS982- DXS6811-DXS8093-AFM240xblO- DXS75-DXS737-DXS100-DXS6-DXS1046-DXS803 8. The order of six major markers is confirmed by fluorescent in situ hybridization, and all the markers assigned by linkage mapping fall within a 1.6-cM interval. The contig comprises 90 clones containing 89 STSs, yielding a resolution of 50 kb; DNA in a gap just telomeric to DXS8044 has not been found in > 20 equivalents of YACs or bacterial clones. The two deletions were found to have centromeric breakpoints that lie close to DXS1206 and may be identical; the telomeric breakpoints are -150 kb apart, one falling between DXS737 and DXS100, the other between DXS100 and DXS1046. Several STSs near the breakpoints show weak amplification from more than one site; one gives products from three groups of YACs, and lie, respectively, within 50 kb of the centromeric and the two telomeric deletion borders. Such partially duplicated segments of DNA are candidates for involvement in the formation of the deletions.

Analysis of the 5' end of the rat plasma membrane Ca(2+)-ATPase isoform 3 gene and identification of extensive trinucleotide repeat sequences in the 5' untranslated region

We have characterized the 5' end of the rat gene encoding isoform 3 of the plasma membrane Ca(2+)-ATPase using S1 nuclease protection and DNA sequence analysis. The 5'-untranslated region consists of over 900 nucleotides and includes a 217-nucleotide sequence composed of alternating tracts of TCC and ACC trinucleotides. Analysis of genomic sequences 5' to the transcription initiation site revealed potential binding sites for transcription factors that are active in muscle and brain.

A putative human equivalent of the murine Xlr (X-linked, lymphocyte-regulated) protein

The murine Xlr (X-linked, lymphocyte-regulated) gene family was originally identified by subtractive cDNA hybridization and cloning. It was found to encode two 30-kDa nuclear proteins expressed in lymphoid cells and in primary spermatocytes in a developmentally regulated manner. Our data show that, in contrast to most X-linked genes, the Xlr family is not conserved at the DNA level between mouse and human. However, using anti-Xlr antibodies, an Xlr-immunoreactive nuclear protein of M(r) 30,000 was characterized in human RAJI B-lymphoblastoid cells by flow cytofluorimetry, by immunoblotting, and by immunocytolabeling. An Xlr-like molecule was also found to be expressed in human activated lymphocytes and in human primary spermatocytes, with a stage specificity similar to that known in the mouse. In contrast, no Xlr-immunoreactive protein was detected in a series of human tissues including brain, skeletal muscle, colon, liver, and kidney, revealing a tissue-specific expression pattern similar to that of murine Xlr. These findings most likely identify a human equivalent of Xlr. The Xlr genes belong to a small category of X-linked genes, including STS, MIC2, CSF2RA, and KAL, that diverge at the DNA level in human and in mice. Characterization of the human XLR gene(s) should now be feasible with anti-Xlr antibodies and an expression cloning system. It should provide new insights into the evolution of mammalian X Chromosome (Chr).

Short tandem repeat polymorphism linkage studies in a new family with X-linked mental retardation (MRX20)

A family with X-linked recessive mental retardation (XLMR) without other obvious manifestations (MRX20) was studied with 14 short tandem repeat polymorphism (STRP) markers. Two-point lod scores above 3 were obtained with DXS1003, DXYS1, DXS3, and DXS458. A multipoint lod score of 4.25 was obtained with peak at DXS1003. Recombination events identify a 55.6 cM interval between DXS1068 and DXS454, while a one unit support interval identifies 40 cM between MAOA and DXS458.

Designer genes and critical care nursing: the future is now

Discoveries about the human genetic code and innovations to manipulate genes are rapidly advancing. Laboratory strategies used for recombinant deoxyribonucleic acid techniques have revolutionized medication production and have led to experimental protocols for gene therapy. The implications for critical care nursing practice are profound. To keep pace with new discoveries, critical care nurses now need to consider the impact of advances in genetic engineering on their practice. Nurses assisting with gene therapy protocols will need to not only update their knowledge of genetics but also learn the fundamentals of recombinant technology. Administration of genetically engineered medications almost certainly will lead to new clusters of side effects and new routes for delivery. A multitude of ethical considerations such as biosafety and patient selection raises a realm of clinical practice implications. To provide the care that critically ill patients require, practitioners will need to update their knowledge constantly about the rapidly changing discipline of genetics and how advances in genetics relate to nursing and medical practice.

Sequence and gene content in 52 kb including and centromeric to the G6PD gene in Xq28

A cosmid containing 36.4 kb of high GC human DNA centromeric to the G6PD gene has been analyzed. The sequence was 99.9% precise, based on the comparison of 4.3 kb that overlaps an earlier analysis of 20.1 kb containing G6PD. Properties of the entire 52 kb region that may be characteristic of high GC portions of the genome include a very high density of sixty-two half or full Alu sequences, or 1.2/kb, and an absence of L1 sequences. Other highly repetitive sequences include 11 MER sequences, one of them interrupted at two positions by groups of 3 Alu elements. In segments of unique sequence, computer-aided analysis predicted three possible genes, one of which has thus far been confirmed by the recovery of a corresponding cDNA, both by a direct hybridization method and by a PCR-based method based on a primer pair inferred from the genomic sequence. The cDNA has been sequenced, and is completely concordant with counterpart genomic sequence; it has no resemblance to any previously described gene.

XLMR genes: update 1994

We provide a comprehensive list of all known forms of X-linked mental retardation. It comprises 127 entries, subdivided into 5 categories (syndromes, dominant disorders, metabolic disorders, neuromuscular disorders, and nonspecific mental retardation). Map location of 69 putative loci demonstrates several overlaps, which will only be resolved by more refined mapping or cloning of the respective genes. The ultimate goal of identifying all the genes on the X chromosome whose mutations cause mental retardation will require a concerted effort between clinical and molecular investigators.

Identification of tissue-specific expressed sequences in human band Xq28 with complex pig cDNA probes

As a part of the functional analysis of the region from the position of the fragile X mutation to the telomere of the long arm of the human X Chromosome (Chr), we have developed a number of different approaches to identify genes located in this area. We describe here a procedure allowing the rapid identification of expressed sequences based on the hybridization of radioactively labeled complex cDNA probes derived from different pig and human tissues to cosmid clones gridded onto nylon filters and to restriction fragments of these clones. This technique has allowed the identification of a number of differentially expressed sequences in cosmid clones covering most of the Xq27.3 to Xqter region. Using these sequences as hybridization probes, cDNA clones for new genes expressed in a tissue-specific manner were isolated. Applied to genomic regions defined by overlapping cosmid clones, this method will serve as a major component in our strategy to establish integrated physical and transcription maps.

Homologous loci DXYS156X and DXYS156Y contain a polymorphic pentanucleotide repeat (TAAAA)n and map to human X and Y chromosomes

We report the isolation and characterization of a polymorphic pentanucleotide repeat (TAAAA)n, which was mapped to human chromosomes X and Y (loci DXYS156X and DXYS156Y) by PCR amplification of DNA from a monochromosomal somatic cell hybrid panel (NIGMS panel 2). The (TAAAA)n repeat of loci DXYS156 occurs within a human LINE element at a position where the consensus sequence contains a single TAAAA motif. In 72 unrelated CEPH individuals seven alleles were detected which ranged in size from 125 to 165 bp in 5 bp intervals. The two largest alleles (160 and 165 bp) were observed only in males, which suggests that they were amplified from the Y chromosome DXYS156Y locus. The other 5 alleles were present in two copies in females and in a single copy in males, which suggests that they were amplified from the X chromosome DXYS156X locus. Locus DXYS156X was polymorphic in CEPH families with an observed heterozygosity in females of 46% (27 of 59). Linkage analysis with DNA markers on the X chromosome revealed significant lod scores for a location of DXYS156X close to markers DXS1002 (theta = 0.000; zeta = 8.43), DXYS1X (theta = 0.015; zeta = 17.3), DXS3, and PGK1 in the region of chromosome Xq13. The sequence of DXYS156Y derived from the 165 bp allele has been deposited in Genbank with accession number X71600.

Gene mapping of the mammalian genome: the CEPH and Genethon initiative

Over the past four years, the CEPH (Jean Dausset Foundation) has expanded its linkage mapping effort to include physical mapping and, in 1990, co-founded the Genethon to ensure that a combined physical and genetic map of the entire human genome would be achieved. The Genethon has applied methods developed at CEPH on an industrial scale to accomplish the colossal task of constructing an integrated map. It is the role of such an integrated map to accelerate the search for the genes responsible for inherited diseases, and the results of the past 12 months encourage our optimism that this goal will be realized rapidly. These discoveries are providing not only an approach to the diagnosis of genetically based disease but also some of the first breakthroughs in the area of gene therapy.

Transcriptional organization of a 450-kb region of the human X chromosome in Xq28

In this paper, we report the transcriptional organization of a 450-kb gene cluster in Xq28, flanked by the glucose-6-phosphate dehydrogenase and the color vision genes. CpG islands previously identified and mapped to distal Xq28 have helped in construction of a continuous contig of cosmids and in identification of cDNAs corresponding to eight transcripts. Thirteen to 16 small genes with CpG islands are clustered in a region of 250-300 kb. Many are highly expressed in muscle or brain and may be the genes responsible for muscle or neurological disorders mapped to distal Xq28. Our analysis indicates that, in this region of the genome, genes not related in sequence are organized in transcriptional domains of 100 kb and that this organization may be important for establishing and regulating gene expression in relation to tissue distribution and X chromosome inactivation.

Adrenoleukodystrophy gene: unexpected homology to a protein involved in peroxisome biogenesis

Adrenoleukodystrophy (ALD) is an X-linked peroxisomal disorder characterized by a progressive demyelination of the central nervous system and adrenal insufficiency. Clinical phenotypes of different severity are frequently observed within the same kindred. ALD is characterized biochemically by the accumulation of very-long-chain fatty acids (VLCFA) due to an impairment in the beta-oxidation of these fatty acids in peroxisome. From the observation that oxidation of VLCFA-CoA is normal in fibroblasts from patients with ALD, it was concluded that the gene coding for VLCFA-CoA synthetase was a candidate gene for ALD. Using positional cloning strategies, we have identified a gene which was found partially deleted in 7% of 85 independent patients with ALD. The predicted protein (ALDP) sequence shows significant homology to the 70-kDa peroxisomal membrane protein which is involved in peroxisome biogenesis and belongs to the 'ATP binding' superfamily of transporters. ALDP thus encodes a putative peroxisomal transporter molecule which may be involved in the import or anchoring of VLCFA-CoA synthetase.