Nonsense mutations in the OCRL-1 gene in patients with the oculocerebrorenal syndrome of Lowe

A candidate gene, OCRL-1, for the oculocerebrorenal syndrome of Lowe (OCRL) has been identified via positional cloning strategies. We have now developed RT-PCR techniques which allow amplification of nearly all of the open reading frame from total RNA and have used the PCR products for mutational analysis. Single strand conformational polymorphism analysis detected aberrant migration in two unrelated patients, both of whom were shown to have the same nonsense mutation at base 2746 on direct sequencing. An additional patient was found to be missing a segment from his RNA that corresponds to an entire exon. The identification of mutations in the OCRL-1 gene provides strong genetic evidence for its being the gene involved in Lowe syndrome.

Deletion mapping and a highly reduced radiation hybrid in the Xp22.3-p22.2 region

The human Xp22.3-p22.2 region contains several known disease genes as well as distinctive families of low copy repetitive sequences. In this study, we have developed new tools to more finely map this area. We have characterized a mapping panel of various cell lines and hybrids with different molecular breakpoints as defined by previously mapped reference markers from this region. The panel subdivides this area into nine distinct regions from DXS41 through the pseudoautosomal boundary. We have also identified a radiation-reduced somatic cell hybrid, Z4-7, that contains DXS31, DXS452, STS, DXS143, and DXS85, but not PABX, DXS16, or other single-copy probes from proximal Xp and Xq. A phage library was constructed from Z4-7 and over 80,000 plaques were screened with total human DNA. More than 100 positive clones were identified as potential new markers in this region. Nine of these have been mapped to the hybrid panel, and unique subclones have been isolated from three of these markers. The panel has also allowed us to map several other DNA markers, genes (AMG, OA1), and repetitive elements of the DXF22S and DXF30S sequence families relative to the various breakpoints.

Cloning of human and bovine homologs of SNF2/SWI2: a global activator of transcription in yeast S. cerevisiae

We performed positional cloning of genes carried on yeast artificial chromosomes that span a human translocation breakpoint associated with a human disease and isolated by chance human and bovine genes with strong homology to the S. cerevisiae genes, SNF2/SWI2 and STH1, and the D. melanogaster gene brahma. We report here sequence analysis, expression data, and functional studies for this human SNF2-like gene (hSNF2L) and its bovine homolog (bovSNF2L). Despite strong homology at the amino acid level, hSNF2L is not capable of complementing the yeast mutations snf2 or sth1 in S. cerevisiae. Furthermore, in contrast to SNF2 itself, a fusion protein consisting of the DNA binding domain of LexA and hSNF2L did not transactivate a reporter gene downstream of LexA binding sites in a yeast expression system. The strong similarity between hSNF2L and these yeast and drosophila genes suggest that the mammalian genes are part of an evolutionarily conserved family that has been implicated as global activators of transcription in yeast and fruitflies but whose function in mammals remains unknown.

The Lowe's oculocerebrorenal syndrome gene encodes a protein highly homologous to inositol polyphosphate-5-phosphatase

Lowe's oculocerebrorenal syndrome (OCRL) is a human X-linked developmental disorder of unknown pathogenesis and has a pleiotropic phenotype affecting the lens, brain and kidneys. The OCRL locus has been mapped to Xq25-q26 by linkage and by finding de novo X; autosome translocations at Xq25-q26 in two unrelated females with OCRL. Here we use yeast artificial chromosomes with inserts that span the X chromosomal breakpoint from a female OCRL patient in order to isolate complementary DNAs for a gene that is interrupted by the translocation. We show that the transcript is absent in both female OCRL patients with X; autosome translocations and that it is absent or abnormally sized in 9 of 13 unrelated male OCRL patients with no detectable genomic rearrangement. The open reading frame encodes a new protein with 71% similarity to human inositol polyphosphate-5-phosphatase. Our results suggest that OCRL may be an inborn error of inositol phosphate metabolism.

Maximum-likelihood analysis of human T-cell X chromosome inactivation patterns: normal women versus carriers of X-linked severe combined immunodeficiency

Lymphocytes of female carriers of X-linked severe combined immunodeficiency (XSCID; McKusick 300400; HGM genetic locus designation SCIDX1) exhibit nonrandom X chromosome inactivation. This phenomenon reflects a tissue-specific selective disadvantage for lymphocyte progenitors with an XSCID mutation on the active X chromosome and presumably is analogous to the process that inhibits T-cell development in affected boys with a single XSCID-bearing X chromosome. We investigated the specificity of T-cell X chromosome inactivation pattern as an indicator of immunodeficiency carrier status, as follows: X-inactivation ratios determined in a control group of noncarrier women exhibited a wide range, 20%-86% of T-cells with the paternal X active. Maximum-likelihood analysis of these data suggested that, in humans, mature T-cells are derived from a small pool of only about 10 randomly inactivated stem cells. Despite the wide variability in normal X-inactivation ratios, X inactivation in XSCID carriers appeared far more markedly skewed. Therefore a maximum-likelihood odds-ratio test was developed and proved to be successful in predicting the carrier status of women in XSCID pedigrees. This test has made it possible to identify XSCID carriers among mothers of boys with the heterogeneous syndrome of sporadic severe combined immunodeficiency.

Isolation of a candidate gene for choroideremia

Choroideremia is an X chromosome-linked retinal dystrophy of unknown pathogenesis. We have isolated cDNAs from a human retinal library with a genomic probe located at the X chromosomal breakpoint in a female with choroideremia and an X;13 translocation. This cDNA spans the breakpoint in the X;13 translocation female and is deleted in males who have choroideremia as part of a complex phenotype including mental retardation and deafness. However, this cDNA detects no alterations in the DNA of 34 males with isolated choroideremia. Nonetheless, the cDNA does detect reduced or absent levels of mRNA in three-quarters of male patients with an apparently intact gene. These data support the hypothesis that this cDNA represents the gene in which mutations cause choroideremia.

Construction and characterization of a yeast artificial chromosome library for Xpter-Xq27.3: a systematic determination of cocloning rate and X-chromosome representation

We describe the construction and characterization of a human X-chromosome-specific yeast artificial chromosome (YAC) library. Starting with 60 micrograms of hybrid cell line genomic DNA, we generated over 150,000 recombinants, over 90% of which range from 150 to 500 kb. From these recombinants, 3300 human-positive YACs (representing coverage of 4.5 X chromosomes) were identified by genomic human DNA hybridization. Mapping of random clones revealed that they are derived from the X chromosome in a regionally unbiased fashion, and screening with single-copy X-chromosome probes has repeatedly produced YACs from the library. By determining the frequency of YAC clones containing both hamster and human repetitive sequences, we estimated that approximately 11% of clones contain discontiguous sequences. Taken together, the low cocloning rate, the unbiased coverage, and a consistent recovery of YACs using specific X-chromosome markers indicate that YAC technology can be used for extensive cloning and mapping purposes. Because a certain amount of genomic rearrangement is present in YAC libraries, chromosome walking must be undertaken with a degree of caution.

Isolation of cDNA sequences around the chromosomal breakpoint in a female with Lowe syndrome by direct screening of cDNA libraries with yeast artificial chromosomes

The Lowe oculocerebrorenal syndrome (OCRL; McKusick 309000) is an X-linked disorder characterized by congenital cataracts, muscular hypotonia, mental retardation, and Fanconi syndrome of the renal tubules. A pair of yeast artificial chromosomes (YACs) that span the Xq25-q26 translocation breakpoint in a female with OCRL were used as probes to screen cDNA libraries made from bovine lens and human kidney. The methods used to prepare the YACs as probes and to screen the libraries are presented in detail. Two different transcripts were found that map to the region around the Xq25-q26 breakpoint. These transcripts are now being studied to determine whether one or the other is a candidate gene for OCRL.

Linkage analysis in X-linked ocular albinism

We studied the linkage of X-linked Nettleship-Falls ocular albinism (OA1) to Xp22.1-Xp22.3 RFLPs at 12 loci in five families, including one in which OA1 cosegregates with a deletion of steroid sulfatase (STS). We found evidence for tight linkage of OA1 to the Xp22.3 loci DXS143, STS, and DXS452. DXS452, a newly described polymorphism detected by the probe E25B1.8, is part of the sequence family "DXS278" (pCRI-S232), but represents a single genetic locus. Every female in this study was heterozygous for the DXS452 RFLP. Thus, this marker will be extremely useful for family studies and genetic counseling. Analysis of individual recombinations suggests that OA1 maps between DXS143 and DXS85. Multipoint linkage analysis was consistent with this localization but was not statistically significant. These data suggest that OA1 lies proximal to the deletion in a previously described family with OA1 and STS deletion, but maps within the Xp22.3-Xp22.2 region.

Partial deletions of a sequence family ("DXS278") and its physical linkage to steroid sulfatase as detected by pulsed-field gel electrophoresis

pCRI-S232 (DXS278) is a 7-kb genomic sequence that hybridizes to multiple polymorphic X-linked restriction fragments on standard Southern analysis. Physical mapping of pCRI-S232 by pulsed-field gel electrophoresis (PFGE) suggests that a sequence in S232 is repeated in multiple X-chromosomal regions in normal individuals. Steroid sulfatase (STS) and DXS237 each hybridize to two of six X-linked SfiI fragments detected by S232. Two independent familial STS deletions, one of which is associated with a phenotype of ichthyosis plus ocular albinism (XI/OA1) and the other with nystagmus plus Rud syndrome, lack some but not all of the normal S232 PFGE fragments. We isolated a DNA fragment, E25B1.8, from a cosmid that contains S232. E25B1.8 detects a subset of the S232 polymorphic fragments on standard Southern blots plus new constant fragments; some, but not all, of the E25B1.8-hybridizing fragments are deleted in the XI/OA1 and Rud syndrome/nystagmus males. The simpler, but highly informative, polymorphism detected by E25B1.8 (DXS452) also eliminates an "intralocus" recombination seen with S232. We conclude that (1) males with STS deletions and complex phenotypes are partially deleted for DXS278, (2) DXS237 and part of DXS278 lie within 800 kb of STS, and (3) a repeat sequence within or around pCRI-S232 is probably located in multiple X-chromosomal locations spanning at least 2-3 Mb.

Genetic and physical mapping of Xq24-q26 markers flanking the Lowe oculocerebrorenal syndrome

The Lowe oculocerebrorenal syndrome (OCRL) is characterized by congenital cataract, mental retardation, and renal tubular dysfunction. We are using the approaches of linkage analysis, mapping with somatic cell hybrids, and long-range restriction mapping to determine the order of Xq24-q26 markers with respect to each other and to the OCRL locus. DXS42 and DXS100 are proximal to the translocation breakpoint in a female patient with OCRL and a de novo translocation t(X;3)(q25;q27). DXS10, DXS86, HPRT, and DXS177 are distal to the breakpoint. These flanking markers show tight linkage to the disease locus in 11 families segregating for OCRL. Results from field inversion gel analysis show that DXS86 and DXS10 share a 460-kb BssHII fragment. Multipoint analysis to determine the position of HPRT with respect to (DXS10,DXS86) suggests that HPRT is proximal to (DXS10,DXS86). We propose the following order for markers in Xq24-q26: Xcen-(DXS42,DXS37,DXS100)-OCRL-DXS53 -HPRT-[(DXS10,DXS86),DXS177]-Xqter. The identification of additional tightly linked flanking markers extends the number of markers available for use in genetic counseling and begins to define the physical map of the region containing the gene for OCRL.

Linkage studies and deletion screening in choroideremia

Fourteen families with choroideremia (TCD) have been examined for linkage to nine genetic markers located on the proximal long arm of the X chromosome. Linkage to three markers (DXYS1, DXS72, DXS3) located in Xq21 was found with a four point lod score of 8.25. No evidence of submicroscopic deletions was observed using DXS233 and DXS232, both thought to lie within about 1 Mb of the TCD gene.

Heterogeneity of clinical severity and molecular lesions in Aicardi syndrome

All patients with Aicardi syndrome are female or have a 47,XXY karyotype. This finding, along with a report of an Aicardi syndrome patient with an Xp22/autosome translocation, led to the hypothesis that Aicardi syndrome might be caused by an X-linked dominant, male-lethal mutation on the short arm of the X chromosome. To study this hypothesis, we investigated X chromosome inactivation patterns in peripheral lymphocytes from seven patients. We used two methods: methylation-sensitive restriction enzyme analysis and segregation of the active X chromosome in somatic cell hybrids. We found that three of seven cytogenetically normal girls with Aicardi syndrome had profoundly skewed X-inactivation in their lymphocytes, supporting the concept that Aicardi syndrome is X linked. Three of the five girls with the greatest degree of psychomotor retardation and the poorest seizure control had skewed X-inactivation. In contrast, the two highest-functioning children had random X-inactivation. We screened DNA using eight polymorphic probes from the Xp22 region but were unable to identify a deletion in any of the seven patients. Nonrandom X-inactivation in lymphocytes and possibly other tissues in some, but not all, patients with Aicardi syndrome may reflect heterogeneity of their molecular lesions.

DXS165 detects a translocation breakpoint in a woman with choroideremia and a de novo X; 13 translocation

The search for the gene for choroideremia (MIM 30310), a rare retinal dystrophy, has been of great interest due to the existence of several choroideremia patients with well-defined structural chromosome aberrations, thus providing the basis for a reverse genetics approach to the isolation of this disease gene. This report details our molecular studies of a woman with choroideremia and a de novo X; 13 translocation. Pulsed-field gel electrophoresis using a contour-clamped homogeneous electric field apparatus has allowed detection of the translocation breakpoint with the anonymous DNA marker p1bD5 (DXS165) and the mapping of this probe to within 120 kb of the breakpoint. In addition, we have used this probe to isolate a clone (pCH4) from a 100-kb jumping library which has crossed a rare-cutting restriction site (XhoI) between DXS165 and the choroideremia gene and detects the translocation breakpoint using this enzyme. Although DXS165 lies within 120 kb of the breakpoint and Cremers et al. (1987, Clin. Genet. 32: 421-423; 1989, PNAS 86: 7510-7514) have detected deletions of DXS165 in 3 of 30 choroideremia probands, we have detected no deletions of this marker or of pCH4 in 42 unrelated probands with this retinal disease.

Mapping X-linked ophthalmic diseases. IV. Provisional assignment of the locus for X-linked congenital cataracts and microcornea (the Nance-Horan syndrome) to Xp22.2-p22.3

The Nance-Horan syndrome (NHS) is an infrequent X-linked disorder typified by dense congenital central cataracts, microcornea, anteverted and simplex pinnae, brachymetacarpalia, and numerous dental anomalies. The regional location of the genetic mutation causing NHS is unknown. The authors applied the modern molecular techniques of analysis of restriction fragment length polymorphisms to five multigenerational kindreds in which NHS segregated. Provisional linkage is established to two DNA markers--DXS143 at Xp22.3-p22.2 and DXS43 at Xp22.2. Regional localization of NHS will provide potential antenatal diagnosis in families at risk for the disease and will enhance understanding of the multifaceted genetic defects.

An arginine to glutamine mutation in residue 109 of human ornithine transcarbamylase completely abolishes enzymatic activity in Cos1 cells

Ornithine transcarbamylase (OTC) is an important enzyme in the detoxification of ammonia to urea, and its deficiency is the most common inborn error of ureagenesis in humans. Among 24 cases of OTC deficiency previously examined, three unrelated individuals all showed loss of a Taq I site in the OTC gene corresponding to codon 109, suggesting that this Taq I site may be prone to mutation. Two of these patients demonstrated the same C----T transition (in antisense strand) converting Arg109 to Gln. Although these studies implied a strong association between the missense mutation and OTC-deficient phenotype, a causal relationship could not be firmly established. We have investigated this relationship by reconstructing the mutation in vitro. A full-length human OTC cDNA was cloned into an SV40-based expression vector and has been reproducibly expressed at high levels in the cell line Cos1. By site-directed mutagenesis of this wild type sequence, we constructed a missense mutation which contains the C----T transition. Electroporation and transient assay in Cos1 indicated that the specific activity of mutant OTC was 100-fold lower than that of wild type. This result confirms that the Taq I alteration leading to the Gln missense is responsible for the OTC deficiency affecting the above patients.

An Xp22 microdeletion associated with ocular albinism and ichthyosis: approximation of breakpoints and estimation of deletion size by using cloned DNA probes and flow cytometry

Ocular albinism of the Nettleship-Falls type (OA1) and X-linked ichthyosis (XI) due to steroid sulfatase (STS) deficiency are cosegregating in three cytogenetically normal half-brothers. The mother has patchy fundal hypopigmentation consistent with random X inactivation in an OA1 carrier. Additional phenotypic abnormalities that have been observed in other STS "deletion syndromes" are not present in this family. STS is entirely deleted on Southern blot in the affected males, but the loci MIC2X, DXS31, DXS143, DXS85, DXS43, DXS9, and DXS41 are not deleted. At least part of DXS278 is retained. Flow cytometric analysis of cultured lymphoblasts from one of the XI/OA1 males and his mother detected a deletion of about 3.5 million bp or about 2% of the X chromosome. Southern blot and RFLP analysis in the XI/OA1 family support the order tel-[STS-OA1-DXS278]-DXS9-DXS41-cen. An unrelated patient with the karyotype 46,X,t(X;Y) (p22;q11) retains the DXS143 locus on the derivative X chromosome but loses DXS278, suggesting that DXS278 is the more distal locus and is close to an XI/OA1 deletion boundary. If a contiguous gene deletion is responsible for the observed XI/OA1 phenotype, it localizes OA1 to the Xp22.3 region.

Choroideremia and deafness with stapes fixation: a contiguous gene deletion syndrome in Xq21

The study of contiguous gene deletion syndromes by using reverse genetic techniques provides a powerful tool for precisely defining the map location of the genes involved. We have made use of individuals with overlapping deletions producing choroideremia as part of a complex phenotype, to define the boundaries on the X chromosome for this gene, as well as for X-linked mixed deafness with perilymphatic gusher (DFN3). Two patients with deletions and choroideremia are affected by an X-linked mixed conductive/sensorineural deafness; one patient, XL-62, was confirmed at surgery to have DFN3, while the other patient, XL-45, is suspected clinically to have the same disorder. A third choroideremia deletion patient, MBU, has normal hearing. Patient XL-62 has a cytogenetically detectable deletion that was measured to be 7.7% of the X chromosome by dual laser flow cytometry; the other patient, XL-45, has a cytogenetically undetectable deletion that measures only 3.3% of the X chromosome. We have produced a physical map of the X-chromosome region containing choroideremia and DFN3 by using routine Southern blotting, chromosome walking and jumping techniques, and long-range restriction mapping to generate and link anonymous DNA sequences in this region. DXS232 and DXS233 are located within 450 kb of each other on the same SfiI and MluI fragments and share partial SalI fragments of 750 and greater than 1,000 kb but are separated by at least one SalI site. In addition, DXS232, which lies outside the MBU deletion, detects the proximal breakpoint of this deletion. We have isolated two new anonymous DNA sequences by chromosome jumping from DXS233; one of these detects a new SfiI fragment distal to DXS233 in the direction of the choroideremia gene, while the other jump clone is proximal to DXS233 and detects a new polymorphism. These data refine the map around the loci for choroideremia and for mixed deafness with stapes fixation and will provide points from which to isolate candidate gene sequences for these disorders.

RFLPs in human X-linked PGK1: a new probe for the PstI RFLP demonstrates strong linkage disequilibrium with the BgII RFLP

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Detection of translocation breakpoints by pulsed field gel analysis: practical considerations

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Linkage analysis of seven kindreds with the X-linked lymphoproliferative syndrome (XLP) confirms that the XLP locus is near DXS42 and DXS37

Analysis of seven kindreds indicates that the XLP locus exhibits 1% recombination with DXS42 (lod = 17.5) and no recombination with DXS37 (lod = 13.3).

X-linked severe combined immunodeficiency: localization within the region Xq13.1-q21.1 by linkage and deletion analysis

X-linked severe combined immunodeficiency (SCID) (McKusick 30040; IMD4) is a disease of unknown pathogenesis characterized by severe and persistent infections from early in life that are due to absence of both cellular and humoral immune function. Although the disease has been provisionally mapped to proximal Xq, high lethality and lack of a carrier test have limited the number of scorable meioses. We performed linkage analysis in six new kindreds with X-linked SCID, using a random pattern of T-cell X inactivation to rule out the carrier state in at-risk women. Our linkage results, combined with analysis of Xq interstitial deletions, confirmed the regional assignment of X-linked SCID, narrowed the boundaries within which this locus lies to Xq13.1-q21.1, and established the locus order DXS159-(PGK1, SCID)-DXS72-DXS3, defining flanking markers for prenatal diagnosis and carrier testing.

Linkage analysis of a large Latin-American family with X-linked retinitis pigmentosa and metallic sheen in the heterozygote carrier

An extended linkage analysis was performed on the large Latin-American kindred with X-linked retinitis pigmentosa (XLRP) and metallic sheen in the heterozygous carrier studied and reported previously by R.L. Nussbaum et al. (1985, Hum. Genet. 70:45-50) and on a smaller family with the same XLRP variant. In these kindreds the XLRP locus shows close linkage with Xp21 marker loci OTC and DXS206. The results of this linkage analysis agree with the observations made by Nussbaum et al. (1985) that an XLRP locus is distal to DXS7.

New polymorphisms at the DXS98 locus and confirmation of its location proximal to FRAXA by in situ hybridization

The locus DXS98, detected with the 1.5-kb anonymous probe p4D-8, was recently shown to be closely linked and proximal to the locus for the fragile X syndrome, with theta = .05 at lod = 3.406, by utilizing a limited number of meioses informative for a two-allele MspI RFLP. Because DXS98 may be the closest available marker to the fragile X locus (FRAXA), we sought to increase its utility for linkage studies by extending its PIC and confirming its localization to Xq27, proximal to FRAXA. We have isolated 15 kb of genomic DNA (lambda 4D8-3) from the DXS98 locus by using p4D-8 to screen a genomic phage library containing partial Sau3A-digested human DNA. Three additional RFLPs for the enzymes BglII and XmnI were found by using the entire lambda 4D8-3 as probe. Combined heterozygosity for the four RFLPs in 25 unrelated females was 48%, as compared with only 28% when the MspI RFLP alone was used. In situ hybridization of unique sequences from lambda 4D8-3 was performed on metaphase chromosomes of lymphocytes and lymphoblasts from patients with the fragile X syndrome. Grains on the X chromosome were significantly clustered at band Xq27. Following fragile site induction, all nine grains in the q27-28 region were proximal to the fragile site. Confirmation of the location of DXS98 proximal to FRAXA and the new RFLPs at this locus make DXS98 more useful for linkage analysis and physical mapping in the region of the fragile X mutation.

Physical fine mapping of the choroideremia locus using Xq21 deletions associated with complex syndromes

Characterization of several male-viable deletions and duplications with 20 random DNA probes has enabled us to subdivide the Xq21 region into seven discernible intervals. Almost all of the deletions spanning part of Xq21 are associated with choroideremia and mental retardation, with deafness being another common feature. The gene locus for choroideremia was assigned to interval 3 spanning the loci DXS95, DXS165, and DXS233. Genes for X-linked deafness and mental retardation were tentatively assigned to interval 2. Deletions of intervals 4 through 7 were not associated with any clinical abnormality. We have constructed a preliminary long-range restriction map of intervals 2 and 3 using field-inversion gel electrophoresis. The DXS232, DXS121, and DXS233 loci are located on the same SfiI fragment, whereas the DXS165 and DXS95 loci could not be linked to this cluster using SfiI and SalI.

Characterization of point mutations in the same arginine codon in three unrelated patients with ornithine transcarbamylase deficiency

Point mutations in the X-linked ornithine transcarbamylase (OTC) gene have been detected at the same Taq I restriction site in 3 of 24 unrelated probands with OTC deficiency. A de novo mutation could be traced in all three families to an individual in a prior generation, confirming independent recurrence. The DNA sequence in the region of the altered Taq I site was determined in the three probands. In two unrelated male probands with neonatal onset of severe OTC deficiency, a guanine (G) to adenine (A) mutation on the sense strand (antisense cytosine [C] to thymine [T]) was found, resulting in glutamine for arginine at amino acid 109 of the mature polypeptide. In the third case, where the proband was a symptomatic female, C to T (sense strand) transition converted residue 109 to a premature stop. These results support the observation that Taq I restriction sites, which contain an internal CG, are particularly susceptible to C to T transition mutation due to deamination of a methylated C in either the sense or antisense strand. The OTC gene seems especially sensitive to C to T transition mutation at arginine codon 109 because either a nonsense mutation or an extremely deleterious missense mutation will result.

Chromosomal localization of the genes for the vitronectin and fibronectin receptors alpha subunits and for platelet glycoproteins IIb and IIIa

The integrins, a family of related membrane receptors involved in cell-cell and cell-matrix interactions, are heterodimeric complexes of alpha and beta subunits. To begin to understand the evolution of these complexes, we studied the genomic organization of several alpha and beta integrin subunits. Using both somatic cell hybrids and an in situ hybridization technique, we have determined the chromosomal location of the genes for the alpha subunits of the vitronectin receptor (VNR alpha), the fibronectin receptor (FNR alpha), and for the alpha subunit of the platelet glycoprotein IIb/IIIa complex, GPIIb. In addition, we have determined the chromosomal location of the gene for the beta subunit of the GPIIb/IIIa heterodimer, GPIIIa. Our studies indicate that the alpha subunits do not localize to a single locus, but that each is found on a different chromosome. The gene for VNR alpha is located on chromosome 2, the gene for FNR alpha is on chromosome 12q11----13, and the gene for GPIIb is on chromosome 17q21----23. In contrast to the chromosomal dispersion of the alpha subunits, the genes for GPIIb and GPIIIa are physically close, with the gene for GPIIIa also located on chromosome 17q21----23. These studies indicate that the genes for the alpha subunits of the integrin family have been dispersed during evolution while GPIIb and GPIIIa are in close physical proximity. This physical proximity of GPIIb and GPIIIa may be involved in the concurrent expression of these proteins by megakaryocytes, and may result in linkage disequilibrium between these two genes, which would limit the use of restriction length polymorphisms in linkage studies of GPIIb/IIIa abnormalities in small kindreds.

Tightly linked flanking markers for the Lowe oculocerebrorenal syndrome, with application to carrier assessment

The Lowe oculocerebrorenal syndrome (OCRL) is characterized by congenital cataract, mental retardation, and defective renal tubular function. A map assignment of OCRL to Xq24-q26 has been made previously by linkage analysis with DXS42 at Xq24-q26 (theta = 0, z = 5.09) and with DXS10 at Xq26 (theta = 0, z = 6.45). Two additional families were studied and three additional polymorphisms were identified at DXS42 by using a 35-kb sequence isolated with the probe detecting the original polymorphism at DXS42. With additional OCRL families made informative for DXS42, theta remained 0 with z = 6.63; and for DXS10 theta = 0.03 and z = 7.07. Evidence for placing OCRL at Xq25 also comes from a female with Lowe syndrome and an X;3 translocation. We have used the Xq25 breakpoint in this patient to determine the position of OCRL relative to the two linked markers. Each derivative chromosome was isolated away from its normal counterpart in somatic cell hybrids. DXS42 was mapped to the derivative chromosome X containing Xpterq25, and DXS10 was mapped to the derivative chromosome 3 containing Xq25-qter. The markers DXS10 and DXS42 therefore show tight linkage with OCRL in six families and flank the Xq25 breakpoint in a female patient with an X;3 translocation. Linkage analysis with flanking markers was used to assess OCRL carrier status in women at risk. Results, when compared with carrier determination by ophthalmologic examination, indicated that the slit-lamp exam can be a sensitive and specific method of carrier determination in many cases.

Isolation of anonymous DNA sequences from within a submicroscopic X chromosomal deletion in a patient with choroideremia, deafness, and mental retardation

Choroideremia, an X-chromosome linked retinal dystrophy of unknown pathogenesis, causes progressive nightblindness and eventual central blindness in affected males by the third to fourth decade of life. Choroideremia has been mapped to Xq13-21 by tight linkage to restriction fragment length polymorphism loci. We have recently identified two families in which choroideremia is inherited with mental retardation and deafness. In family XL-62, an interstitial deletion in Xq21 is visible by cytogenetic analysis and two linked anonymous DNA markers, DXYS1 and DXS72, are deleted. In the second family, XL-45, an interstitial deletion was suspected on phenotypic grounds but could not be confirmed by high-resolution cytogenetic analysis. We used phenol-enhanced reassociation of 48,XXXX DNA in competition with excess XL-45 DNA to generate a library of cloned DNA enriched for sequences that might be deleted in XL-45. Two of the first 83 sequences characterized from the library were found to be deleted in probands from family XL-45 as well as from family XL-62. Isolation of these sequences proves that XL-45 does contain a submicroscopic deletion and provides a starting point for identifying overlapping genomic sequences that span the XL-45 deletion. Each overlapping sequence will be studied to identify exons from the choroideremia locus.

Carrier detection in X-linked severe combined immunodeficiency based on patterns of X chromosome inactivation

The X-linked form of severe combined immunodeficiency (XSCID) is underdiagnosed because no methods have been available for detecting carriers. Although boys with XSCID are deficient in T cells, female carriers are immunologically normal. Carriers' normal immune function would be expected if all their T cells were derived from precursors whose X chromosome bearing the XSCID mutation was inactivated early in embryogenesis. Using somatic cell hybridization to separate the active and inactive X chromosomes and restriction fragment length polymorphisms to distinguish them, we have determined the lymphocyte X inactivation pattern in XSCID carriers and their female relatives. In the T cells of three carriers, the X chromosome bearing the XSCID mutation was consistently inactive. Nonrandom X inactivation was also found in the T cells of one at-risk female, while two others had normal, random X inactivation. This method constitutes a generally applicable carrier test for XSCID.

Multipoint linkage analysis of loci in the proximal long arm of the human X chromosome: application to mapping the choroideremia locus

Choroideremia (McK30310), an X-linked retinal dystrophy, causes progressive night blindness, visual field constriction, and eventual central blindness in affected males by the third to fourth decade of life. The biochemical basis of the disease is unknown, and prenatal diagnosis is not available. Subregional localization of the choroideremia locus to Xq13-22 was accomplished initially by linkage to two restriction-fragment-length polymorphisms (RFLPs), DXYS1 (Xq13-q21.1) and DXS3 (Xq21.3-22). We have now extended our linkage analysis to 12 families using nine RFLP markers between Xp11.3 and Xq26. Recombination frequencies of 0%-4% were found between choroideremia and five markers (PGK, DXS3, DXYS12, DXS72, and DXYS1) located in Xq13-22. The families were also used to measure recombination frequencies between RFLP loci to provide parameters for the program LINKMAP. Multipoint analysis with LINKMAP provided overwhelming evidence for placing the choroideremia locus within the region bounded by DXS1 (Xq11-13) and DXS17 (Xq21.3-q22). At a finer level of resolution, multipoint analysis suggested that the choroideremia locus was proximal to DXS3 (384:1 odds) rather than distal to it. Data were insufficient, however, to distinguish between a gene order that puts choroideremia between DXS3 and DXYS1 and one that places choroideremia proximal to both RFLP loci. These results provide linkage mapping of choroideremia and RFLP loci in this region that will be of use for further genetic studies as well as for clinical applications in this and other human diseases.

Mapping the Lowe oculocerebrorenal syndrome to Xq24-q26 by use of restriction fragment length polymorphisms

A molecular linkage analysis of four large families with the Lowe oculocerebrorenal syndrome (LS) provided a subregional localization of LS to the distal long arm of the X chromosome at Xq24-q26. Probes from two loci that identify restriction fragment length polymorphisms (RFLPs) and map to Xq24-q26 showed no recombination with LS. A maximum likelihood recombination distance (theta) = 0.00 was obtained for DXS10 with the logarithm of the odds (lod) of 6.450. For DXS42, theta = 0.00 with a lod of 5.087. Assignment of the gene or genes for LS to Xq24-q26 has the potential of improving carrier detection and providing prenatal diagnosis in families at risk for the disease.

Implications of fragile X expression in normal males for the nature of the mutation

The fragile site at Xq27, associated with a common form of X-linked mental retardation (XLMR), is expressed in a variable proportion of the peripheral lymphocytes of affected males when the cells are cultured under thymidylate stress (Td stress) produced by folate or thymidylate deprivation. Some clinically normal males--transmitting males--are known to carry and transmit the fragile X mutation and yet show no cytogenetic expression in lymphocytes. Normal males with no family history of X-linked mental retardation express the site only rarely. When the fragile X chromosome from affected males is isolated in a rodent genetic background by somatic cell hybridization, the level of expression is similar to that seen in lymphocytes under Td stress. Here we show that X chromosomes from two transmitting males and two normal control males, all of which were fragile X negative in lymphocytes or lymphoblasts, could be made to express the fragile site in hybrids, although at levels that were below those seen in hybrids from affected males. Furthermore, transmitting males could be differentiated from normal males by their significantly higher expression rates when hybrids were exposed to caffeine before cytogenetic harvest. One male chimpanzee also showed low level expression in hybrid cells. These data suggest that the hybrid system lowers the threshold for fragile X expression, a fragile site at Xq27 may be present on all human and chimpanzee X chromosomes and constitutes a previously unrecognized common fragile site and the hybrid system with caffeine post-treatment can distinguish between the common Xq27 fragile site of control males, the occult mutant fragile site of a transmitting male, and the fully expressed fragile site of an affected male with XLMR. Thus the mutation producing XLMR may represent a multi-step alteration of a naturally occurring DNA sequence producing a continuum of cytogenetic expression and a threshold for clinical manifestation.

New mutation and prenatal diagnosis in ornithine transcarbamylase deficiency

Ornithine transcarbamylase (OTC) (E.C.2.1.3.3) is an X-linked hepatic enzyme in the urea cycle necessary for ammonia detoxification. Deficiency of OTC results in neonatal hyperammonemia, coma, and death in childhood. Because fibroblasts do not express OTC, prenatal diagnosis in the past has required fetal liver biopsy. Using a complementary DNA (cDNA) for OTC for Southern blot analysis of genomic DNA, we have found probands with complete OTC deficiency from two unrelated families in whom the same TaqI restriction endonuclease site has been altered because of independent, but not necessarily identical, mutations in the OTC gene, suggesting that this site may be a relative hotspot for mutation at a location that is critical for normal gene function. This TaqI alteration has allowed the identification of the individual in each family in whom the mutation originated as well as the exclusion of a recurrence of OTC deficiency in a male fetus at risk for the disease. OTC deficiency joins the growing list of genetic disorders for which Southern blot analysis allows accurate heterozygote detection and prenatal diagnosis in conditions for which they were not previously available.

Caffeine enhances fragile (X) expression in somatic cell hybrids

Yunis and Soreng recently demonstrated enhanced expression of common fragile sites as and of fra(X) when 2.2 mM caffeine is added to FUdR treated lymphocyte cultures 6 hours before harvest. We failed to replicate this finding for fra(X) expression in lymphocytes. However, we do find a consistent increase in expression levels in somatic cell hybrids between a Chinese hamster cell line and 3 unrelated individuals with the fra(X) mutation when caffeine is present for the last 2 hours before harvest. This was particularly true for "low-expressing" cell lines, in which a 4-6 fold increase was observed. Using a thymidylate synthase deficient hybrid which could be blocked in the S phase by thymidine deprivation, we found that caffeine significantly reduced the recovery time from thymidine release to mitosis. This produced the highest level of fra(X) expression (48%) only one hour after release from thymidine deprivation. These results show that caffeine does enhance fra(X) expression in at least some cell types. The effect is probably indirect, inhibiting the mitotic delay usually associated with DNA damage.

Somatic cell hybrid studies of fragile (X) expression in a carrier female and transmitting male

We have extended our previous studies of fra(X) expression in somatic cell hybrids to the analysis of a carrier female with a low level of expression and to an unaffected, transmitting male who shows no expression in lymphocytes or lymphoblasts. Optimum conditions for fra(X) expression was treatment with 10(-8) M FUdR for 16 hours. In recent experiments, addition of 2.2 mM caffeine 2 hours before harvest was found to increase expression consistently. Two clones from the carrier female containing the fra(X) chromosome but not the normal X showed expression of 2-4%, indicating that expression in heterozygous females is not influenced by the presence or absence of the normal X. Expression rate was increased to 20% by exposure to FUdR plus caffeine. Analysis of hybrids containing only the fra(X) in an inactive state, and after reactivation by 5-azacytidine, showed no change in the frequency of expression. A hybrid clone from the nonexpressing, transmitting male containing only the X and chromosome 13, showed expression ranging from 2% without caffeine to 12% with caffeine in three different experiments. The ability to induce fra(X) expression in hybrid from this nonexpressing male may be explained in one of several ways: 1) a second mutation has occurred, 2) an autosomal suppressor locus was lost, or 3) the hamster genome or unusually short cell cycle lowers the threshold for expression, particularly in the presence of caffeine.

Recombination and amplification of pyrimidine-rich sequences may be responsible for initiation and progression of the Xq27 fragile site: an hypothesis

HYPOTHESIS

A pyrimidine-rich sequence (PRS) of DNA is present as a normal sequence in the q27 band of the human X chromosome. Under conditions of pyrimidine nucleotide triphosphate deprivation during S phase, deoxyuridine monophosphate is misincorporated and has to be excised during G2 by DNA repair mechanisms. When a simple PRS is present on both homologous X chromosomes during oogenesis, PRS may undergo amplification through non-homologous crossing-over to produce the initial lesion of the fragile (X). Carriers of such initial lesions will be unaffected transmitting females or males. When an X chromosome bearing such an initial lesion is itself paired with a homologous X carrying a simple PRS during oogenesis, a much higher rate of non-homologous crossing-over may occur resulting in progression to an even longer stretch of pyrimidine rich DNA in this region; the increased length of PRS through amplification makes the region too long to be repaired during G2 and allows it to be seen as a fragile site in metaphase chromosome preparations. Furthermore, this amplified lesion may interfere with transcription of one or more genes in this region and produce the phenotype of the Martin-Bell syndrome.

A rodent-human hybrid containing Xq24-qter translocated to a hamster chromosome expresses the Xq27 folate-sensitive fragile site

A somatic cell hybrid containing a single human X chromosome bearing the Xq27 fragile site was lethally irradiated and re-hybridized to its HPRT- Chinese hamster parent. One of 24 colonies surviving selection for HPRT was found to have retained human G6PD but not PGK. This line, X3000-11, which shows Xq24-qter translocated to a hamster chromosome by trypsin G-banding and a single human chromatin fragment corresponding to this segment of the X by G-11 staining, expresses the fragile site on exposure to 5-fluorodeoxyuridine. Dot blots using total human DNA suggest that X3000-11 retains approximately 0.2% of the human genome. By Southern blotting, X3000-11 retains Factor IX, DXS11 and DXS42 but lacks DXYS1, DXS3 and DXS17. This hybrid is being used to construct a cosmid library in the vector pCOS2 from which a sub-library of 500-1000 clones of human origin will be isolated using in vivo recombination with cloned Alu and Kpn family repeats. Such a sub-library will greatly facilitate chromosome walking to the fragile site as well as the testing of individual clones for their ability to create a folate-sensitive fragile site by DNA transfer into permissive Chinese hamster recipient cells.

Thymidylate synthase-deficient Chinese hamster cells: a selection system for human chromosome 18 and experimental system for the study of thymidylate synthase regulation and fragile X expression

Chinese hamster lung (CHL) V79 cells already deficient in hypoxanthine phosphoribosyltransferase were exposed to uv light and selected for mutations causing deficiency of thymidylate synthase (TS) by their resistance to aminopterin in the presence of thymidine and limiting amounts of methyl tetrahydrofolate. Three of seven colonies chosen for initial study were shown to be thymidylate synthase deficient (TS-) by enzyme assay, thymidine auxotrophy, and their inability to incorporate labeled deoxyuridine into their DNA in vivo. Complementation analysis of human X TS- hamster hybrids revealed that TS activity segregated with human chromosome 18. Southern analysis of a panel of 14 human X hamster hybrids probed with complementary DNA from mouse TS confirmed the chromosome assignment of TS to human chromosome 18; quantitative Southern blotting using unbalanced human cell lines further localized the gene to 18q21.31----qter. Another hybrid was generated that contained a human X chromosome with the Xq28 folate-dependent fragile site as its only human chromosome in a hamster TS- background. The fragile site could be easily and reproducibly expressed in this hybrid without the use of antimetabolites simply by removing exogenous thymidine from the medium. These TS-deficient cells are useful for: somatic cell genetics as a unique selectable marker for human chromosome 18, studies on regulation of the TS gene, and analysis of the fragile (X) chromosome and other folate-dependent fragile sites.

Fragile (X) expression induced by FUdR is transient and inversely related to levels of thymidylate synthase activity

Thymidylate synthase (TS) activity was monitored in fluorodeoxyuridine (FUdR)-treated lymphoblasts from individuals carrying the fragile (X) [fra(X)] chromosome. Fra(X) expression and levels of TS activity were measured over a 72-hr period at different cell densities. TS activity was 80%-90% inhibited immediately after exposure to FUdR and remained suppressed for the first 24 hrs. Fra(X) expression was not found until 6-8 hrs after FUdR treatment, and at 24 hrs, reached a maximum expression of approximately 50%. At 48 and 72 hrs, however, increasing levels of TS activity paralleled a dramatic drop in fra(X) expression. High fra(X) expression at 48 and 72 hrs could be maintained by rechallenging cultures with increasing doses of FUdR. At low cell densities, fra(X) expression was maintained at high levels for a much longer period of time. In two lymphoblastoid cell lines from obligate carriers, which either expressed at very low levels or did not express the fra(X) in routine cultures, TS activity was also 90% inhibited but with no corresponding fra(X) expression 12 or 24 hrs after FUdR treatment. We conclude that: FUdR inhibits TS activity immediately and induces fra(X) expression 6-8 hrs later, FUdR-induced fra(X) expression and TS activity are inversely related, the FUdR effect on fra(X) expression and TS activity is time and cell-density dependent, and inhibition of TS activity is a necessary but not sufficient condition for fra(X) expression.

Mapping X-linked ophthalmic diseases. Provisional assignment of the locus for choroideremia to Xq13-q24

Choroideremia (McK 30310), an X-linked hereditary retinal dystrophy, causes nyctalopia, progressive visual field loss, and ultimately central blindness in affected males in early adulthood. We have used restriction fragment length polymorphisms from the X-chromosome to localize the region of the mutation for choroideremia in three families with this disorder. One polymorphic marker, DXYS1, located within Xq13-q21, shows no recombination with choroideremia at a LOD score of 5.78. Thus choroideremia maps within 9 centiMorgans of DXYS1 at 90% probability. Another marker, DXS11, located at Xq24-q26, shows no recombination with choroideremia but at a smaller LOD score of 1.54. These results suggest that the locus for choroideremia is distal to DXYS1 and between the two markers in the region Xq13-q24. This information may be useful for antenatal diagnosis, isolation of the mutant gene, and development of a rational therapy for the disorder.

Choroideremia is linked to the restriction fragment length polymorphism DXYS1 at XQ13-21

Choroideremia (McK30310), an X-linked hereditary retinal dystrophy, causes night-blindness, progressive peripheral visual field loss, and, ultimately, central blindness in affected males. The location of choroideremia on the X chromosome is unknown. We have used restriction fragment length polymorphisms from the X chromosome to determine the regional localization of choroideremia by linkage analysis in families with this disease. One such polymorphic locus, DXYS1, located on the long arm (Xq) within bands q13-q21, shows no recombination with choroideremia at lod = 5.78. Therefore, with 90% probability, choroideremia maps within 9 centiMorgans (cM) of DXYS1. Another polymorphic locus, DXS11, located within Xq24-q26, also shows no recombination with choroideremia, although at a smaller lod score of 1.54 (90% probability limit theta less than 30 cM). This linkage with DXS11, a marker that is distal to DXYS1, suggests that the locus for choroideremia is also distal to DXYS1 and lies between these two markers in the region Xq13-q24. These results provide regional mapping for the disease that may be useful for prenatal diagnosis and, perhaps ultimately, for isolating the gene locus for choroideremia.