Microdeletions of a Y-specific marker, Yfm1, and implications for a role in spermatogenesis

We have detected deletions of a Y-specific microsatellite marker, Yfm1, located on the Y chromosome (Yq) within interval 6 and near the DAZ (deleted in azoospermia) genes, in 9/89 oligospermic and 17/68 azoospermic Japanese men. No Yfm1 deletions were detected in the 150 normal fertile males examined as controls. Yfm1 deletions in the oligo- and azoospermic males were associated with other deletions that removed entire DAZ genes in those infertile men. These deletions indicated that all Yfm1 loci are located within azoospermia factor c (AZFc) in interval 6 on the long arm of the Y chromosome. Mapping Yfm1 on the Y chromosome using the draft sequence of the human genome revealed that at least three Yfm1 loci are located within about 25-30 kbp of the DAZ genes. Moreover, the Yfm1 marker showed the least number of copies in Japanese males derived from a Y chromosomal lineage called haplotype II, defined by having the Y Alu polymorphism (YAP) insertion. Males from this haplotype II lineage are known from our previous studies to have lower spermatogenic abilities, with higher rates of oligo- and azoospermia than other haplotypes. The least number of Yfm1 loci, whose copy number may correspond to that of the DAZ genes, may be a risk factor predisposing an individual to azoospermia or oligospermia.

Disruption of a long-range cis-acting regulator for Shh causes preaxial polydactyly

Preaxial polydactyly (PPD) is a common limb malformation in human. A number of polydactylous mouse mutants indicate that misexpression of Shh is a common requirement for generating extra digits. Here we identify a translocation breakpoint in a PPD patient and a transgenic insertion site in the polydactylous mouse mutant sasquatch (Ssq). The genetic lesions in both lie within the same respective intron of the LMBR1/Lmbr1 gene, which resides approximately 1 Mb away from Shh. Genetic analysis of Ssq reveals that the Lmbr1 gene is incidental to the phenotype and that the mutation directly interrupts a cis-acting regulator of Shh. This regulator is most likely the target for generating PPD mutations in human.

Analysis of DNA polymorphisms on the human Y-chromosome by microchip electrophoresis

Validation of microchip electrophoresis in DNA analysis has been carried out using an Agilent 2100 Bioanalyzer. With a DNA 500 Assay Kit, the reproducibility and accuracy of fragment sizing of a 10 bp DNA ladder have been shown to be satisfactory with the relative standard deviation and the relative error mostly below 1.0 and 5.0% (n = 12), respectively. Both intraday and interday validations of fragment sizing and quantitation have also been performed with a 7500 Assay Kit (n = 48). Although the results of quantitation are not as good as that of sizing, due to the manual introduction of samples and markers into the chip wells, they are still sufficient to carry out further analyses of practical samples. Based on such reliable results, fast analysis of DNA polymorphisms on the human Y-chromosome has been realized with microchip electrophoresis. The total analysis times of three genomic polymorphisms on the Y-chromosome, Y Alu polymorphism, 47z/StuI, and 12f2, are all within 100 s, and the relative standard deviation and relative error of fragment sizes are below 3.5 and 3.7%, respectively. In addition, a mixture of nine DNA markers on the human Y-chromosome related to examine the cause of spermatogenic failure have been separated successfully with the smallest fragment size difference of 7 bp. Our results demonstrate the potential of microchip electrophoresis in polymorphism analysis with the advantages of high speed, good reproducibility, high precision, and high resolution.

Two Y-chromosome-specific polymorphisms 12f2 and DFFRY in the Japanese population and their relations to other Y-polymorphisms

This study of male-specific genetic markers in the Japanese population was carried out in an attempt to refine the existing theories concerning its population genetics and migration events. We examined the relation between the constructed haplotypes of three biallelic Y-chromosome-specific markers (YAP, 47z and SRY) and the results of studying two other Y-specific polymorphisms of both 12f2 and DFFRY markers. The 12f2 marker was completely absent in 14.7% of Japanese males; all of them were haplotype II males. None of the Japanese males from other haplotypes or other East Asian populations showed any deletion of 12f2. In all haplotype II Japanese men, we found that DFFRY gene harbors a (C-->T) substitution polymorphism that was not found in any other population of this study. These results suggested that although haplotype II Japanese males share with the other haplotype II men from different geographical areas in having the YAP insertion on their Y-chromosomes, their Y-chromosomal structure is somewhat characteristically different. They are probably descendants of the ancestral Jomonese population who lived in Japan before the Yayoi immigrants entered Japan approximately 2300 years ago. These findings suggested that linkage studies between Y-specific markers are helpful in understanding the migratory patterns in East Asia. We also suggested that Japanese males have characteristically different Y-chromosomes compared with other populations.

Linkage between prostate cancer incidence and different alleles of the human Y-linked tetranucleotide polymorphism DYS19

We studied the allele frequency distribution of the Y-chromosome linked tetranucleotide polymorphic microsatellite locus DYS19 in 90 prostate cancer Japanese patients from both Tokushima University hospital (Tokushima) and Saint Marianna University hospital (Kawasaki), Japan, comparing them to 99 matched male controls. Y-chromosomes from Japan as well as others from different geographical regions worldwide showed the five different alleles (A-E) with sizes varying from 186-202 bp, respectively. Comparison between DYS19 allelic frequency distribution among Japanese patients with prostate cancer and that of normal controls revealed significant differences regarding susceptibility or resistance to prostate cancer. We found that males with allele C of DYS19 are more susceptible to develop prostate cancer than males with other alleles (p = 0.02). The Odds Ratio was 2.04 with a 95% confidence interval (0.75-2.42), compared with males having other alleles. In contrast, males with the D allele of DYS19 were less exposed to prostate cancer than other males (p = 0.002); the Odds Ratio was 0.26 with a 95% confidence interval of (0.65-3.71). These findings support our hypothesis that male descendants from different Y-chromosomal origins are different regarding their susceptibility or resistance to develop prostate cancer (as a male-specific cancer).

A rapid and simple method for sex identification by heteroduplex analysis, using denaturing high-performance liquid chromatography (DHPLC)

A novel method for sex identification, using a denaturing high-performance liquid chromatography (DHPLC) system, is described. Among many methods for identifying sex, the most popular and credible system has been the polymerase chain reaction (PCR) method, using nucleotide primer sets of the amelogenin gene, which is shared on both the X and Y chromosomes. With this conventional method, the judgment depends on detection of the size difference between the PCR products derived from the X and Y chromosomes. In this study, we adopted DHPLC to detect the difference by checking heteroduplex formation between the products, which enabled us to shorten the PCR products to 45bp and the separation time to within a period of 8min per sample. This new system may have wide applications in many different fields, such as forensic medicine, prenatal diagnosis, inbreeding of animals, and anthropology.

Occupational cancer genetics: infrequent ras oncogenes point mutations in lung cancer samples from chromate workers

BACKGROUND

Chromium carcinogenicity and mutagenicity are no longer disputed. However, although chromium has various genetic effects that induce cancer, its mechanism of inducing lung cancer in humans is still not fully understood. p53, a tumor suppressor gene, was found to be infrequently mutated in samples of lung cancer in workers with long occupational exposure to chromium, suggesting other cancer-related genes to be targeted in such tumors.

METHODS

To assess the contribution of the ras oncogenes in the pathogenesis of chromate-related lung cancer, we studied point mutations at the critical positions of codons 12, 13, and 61 of the Ha-ras and Ki-ras oncogenes in 38 lung cancer samples derived from Japanese patients who worked in the chromate industry for long periods. We used both radioactive isotope and non-radioisotope PCR-SSCP techniques.

RESULTS

The results of this study demonstrated that activation of ras genes due to point mutations in chromate-related lung cancer is a rare event.

CONCLUSIONS

Ras oncogenes activated by point mutations do not have a major role in the process of tumorigenesis of chromate-related lung cancer.

Y chromosome compound haplotypes with the microsatellite markers DXYS265, DXYS266, and DXYS241

Two newly developed microsatellite markers on Yp11 (DXYS265) and Yq11.21 (DXYS266) and our previously reported marker, on Yp11 (DXYS241), were typed by triplex polymerase chain reaction (PCR) in 102 Japanese, 18 white American, and 17 black American males. The DXYS265 locus revealed three alleles, the DXYS266 locus showed two alleles, while the DXYS241 locus showed five alleles. Nine different compound haplotypes were observed among the males. Of these, two haplotypes were common to all groups, while four were limited to Japanese. Pedigree analysis of 61 Japanese families revealed no mutations of these loci. The triplex PCR developed in this study, as well as the new loci, are useful for tracing paternal lineages in human migration studies and population analysis, in addition to Y chromosome evolutionary studies.

Association of a novel constitutional translocation t(1q;3q) with familial renal cell carcinoma

Four cases of late onset clear cell renal cell carcinoma (RCC), a case of gastric cancer, and a case of exocrine pancreatic cancer were identified in a Japanese family. In order to elucidate the underlying mechanism for tumorigenesis in this family, extensive genetic studies were performed including routine and spectral karyotyping (SKY), fluorescence in situ hybridisation (FISH), comparative genomic hybridisation (CGH), loss of heterozygosity studies (LOH), and VHL mutation analysis. A germline translocation t(1;3)(q32-q41;q13-q21) was identified by karyotyping in five members of the family including all three RCC cases tested. The translocation was refined to t(1;3)(q32;q13.3) by FISH analysis using locus specific genomic clones, and the two breakpoints were mapped to a 5 cM region in 3q13.3 and a 3.6 cM region in 1q32. Both CGH and allelotyping using microsatellite markers showed loss of the derivative chromosome 3 carrying a 1q segment in the three familial RCCs analysed. Additional chromosomal imbalances were identified by CGH, including amplifications of chromosomes 5 and 7 and loss of 8p and 9. No germline VHL mutation was found but two different somatic mutations, a splice (IVS1-2A>C) and a frameshift (726delG), were identified in two RCCs from the same patient confirming their distinct origin. Taken together, these results firmly support a three step model for tumorigenesis in this family. A constitutional translocation t(1q;3q) increased the susceptibility to loss of the derivative chromosome 3 which is then followed by somatic mutations of the RCC related tumour suppressor gene VHL located in the remaining copy of chromosome 3.

Pericentric inversion of the Y chromosome of infertile male

The authors report a case with pericentric inversion of the Y chromosome associated with asthenonecrozoospermia. The conventional karyotype was 46, X, inv (Y) (p11q11). Polymerase chain reaction (PCR) analysis revealed the deletion of DYZ3, DYS139, and RBM1. Three-color fluorescent in situ hybridization (FISH) analysis of the sperm chromosomes showed normal ratio between X- and Y-bearing sperm. In this case, the frequencies of aneuploidy of the sperm are not significantly higher compared with those from the normal volunteers. Cytogenetic analysis is recommended when the patients with pericentric inversion of the Y chromosome are attending an infertility clinic.

Spermatogenic ability is different among males in different Y chromosome lineage

It is a controversial question whether sperm concentrations in humans are changing. Several researchers have reported on environmental factors affecting sperm quality, but the influence of genetic factors is still not fully understood. In this study, we examined the relationship between Y chromosome haplotypes and sperm concentration in fertile males. In addition, we determined the haplotypes of azoospermic patients. The results show that the mean sperm concentration correlates with Y chromosome type. Moreover, the occurrence of azoospermia is related to one particular Y chromosome lineage. Thus, males with a certain haplotype are at a disadvantage for fathering children. The difference of spermatogenic ability among men is important not only in pursuing male competition as in the past but also as relates to the future of modern human males.

Structure and chromosome location of human OGG1

OGG1 (alias MMH) encodes an 8-hydroxyguanine glycosylase, functionally homologous to bacterial mutM. Here, we report its genomic structure and fine chromosome location. The human OGG1 gene corresponding to the isoform 1 transcripts, consists of seven exons, spanning 7,421 bps, while an alternative additional exon, utilized for isoform 2, is located approximately 9 kb downstream. TATA-like sequence was not found in the 5'-upstream region, common in so-called "housekeeping" genes. The last 55 bases of the 3' untranslated region in exon 7 were unexpectedly conserved among species, presumably because the 3' end of the CAMK1 gene, which is transcribed convergently on the opposite strand, is overlapped at the 3' end. By radiation hybrid panel mapping, OGG1 was localized between WI-4179 and AFMA216ZG1 at 3p26, proximal to the VHL gene.

Genetic variations on the Y chromosome in the Japanese population and implications for modern human Y chromosome lineage

A polymorphism in the coding sequence of the SRY gene was found by single-strand conformation polymorphism (SSCP) and direct sequencing analysis. The new allele of the SRY gene, which is raised by a C-to-T transition in the 155th codon, was found in 24% of Honshu, 35% of Okinawan, and 51% of Korean males respectively, whereas it was not observed among 16 Caucasian and 18 Negroid males. A haplotype analysis of the Y chromosome was carried out in Japanese, Korean, Caucasian and Negroid populations, using a combination of the polymorphisms in SRY, DXYS5Y, DYS287, and DXYS241Y loci. The results indicated that the Y chromosomes can be classified into seven heplotypes (Ia, Ib, Ic, IIa, IIb, III, IV). However, of these seven, only four (Ia, IIa, III, IV) were observed in the Japanese population. Furthermore, the presumed haplotype C, Y1, YAP, (CA)14, from which haplotype III was probably derived, was not found in any populations in this study. The regional distribution of each haplotype revealed that type III is more frequently observed in Okinawa (16%) and in Korea (21%) than in Honshu (4.4%). The haplotype analysis of the Y chromosome may contribute to the exploration of the origin of Japanese and the relationship between east Asian populations.

Gonadoblastoma, mixed germ cell tumor, and Y chromosomal genotype: molecular analysis in four patients

This study reports on Y chromosomal genotypes of three patients with gonadoblastoma and one patient with gonadoblastoma and mixed germ cell tumor. Molecular analysis for 35 Y chromosomal loci was performed for DNA samples taken from peripheral leukocytes and lymphoblastoid cell lines, showing that the four patients shared the region between DYS267 at interval 4A and DYF50S1 at interval 6D, with the exception of the region around DYS202 at interval 5K. In the patient with gonadoblastoma and mixed germ cell tumor, Y chromosomal material was preserved in the gonadoblastoma but was lost from the mixed germ cell tumor. The results, in conjunction with previous reports, suggest that GBY (gonadoblastoma locus on the Y chromosome) may be located to a roughly 5-Mb pericentromeric region between DYS267 at interval 4A and DYS270 at interval 5A. The presence of Y chromosomal material in gonadoblastoma is consistent with GBY being involved in the development of gonadoblastoma, and the absence of Y chromosomal material in mixed germ cell tumor would be explained as a consequence of Y chromosomal loss from rapidly proliferating gonadal cancer cells.

Novel (CA)n marker DXYS241 on the nonrecombinant part of the human Y chromosome

The origin of modern humans can be traced by comparing polymorphic sites in either mitochondria or genomic sequences between humans and other primates. The human Y chromosome has both a non-recombining region and X-Y homologous pseudo-autosomal regions. In the nonrecombining region events during evolution can be directly detected. At least a part of homology between Xq21 and Yp11 is a result of rather recent translocations from the X chromosome to the Y chromosome. DNA markers residing in the nonrecombining region of the human Y chromosome are potentially useful in tracing male-specific gene flow in human evolution. However, the number of available markers in the region is limited. Here, we report a novel X-Y homologous (CA)n repeat locus in the nonrecombining region of the Y chromosome. This marker, DXYS241, has several interesting features. Y- and X-chromosome alleles are distinguishable because the Y-chromosome alleles are shorter than the X-chromosome alleles most of the time. We developed 2 primer sets for specific examination of Y- and X-chromosome alleles. The marker should be useful in establishing relationships between populations based on patrilineal gene flow. Sequences homologous to DXYS241 are also found on the X chromosome of primates. Four events during primate evolution that led to the modern human Y chromosome were identified.

XX-male syndrome bearing the sex-determining region Y

The case of a 25-year-old man who presented for evaluation of infertility is described. The physical examination revealed testicular atrophy without gynecomastia. Repeated seminal analyses showed azoospermia, and serum hormonal levels suggested a state of a hypergonadotropic hypogonadism. Chromosomal analysis demonstrated 46XX. Polymerase chain reaction revealed the existence of a sex-determining region Y. The etiology of this rare sex reversal syndrome is discussed and cases reported in Japan are reviewed.

New DNA polymorphisms of human MMH/OGG1 gene: prevalence of one polymorphism among lung-adenocarcinoma patients in Japanese

MMH/OGG1 is an 8-hydroxyguanine-specific DNA glycosylase/AP-lyase, one of the mutator enzymes for the excision repair of 8-hydroxyguanine. DNA polymorphisms in human MMH/OGG1 gene were newly identified and analyzed to examine a possible association with lung-cancer risk by a population-based study. Polymorphic allele 3 in hMMH/OGG1 exon 1 was significantly prevalent among Japanese patients with adenocarcinoma of the lung [odds ratio (OR): 3.152, 95% confidence interval (CI): 1.266-7.845], indicating that the excision repair of 8-hydroxyguanine may play a role in predisposition to lung cancer.

New DNA polymorphisms of human MMH/OGG1 gene: prevalence of one polymorphism among lung-adenocarcinoma patients in Japanese

MMH/OGG1 is an 8-hydroxyguanine-specific DNA glycosylase/AP-lyase, one of the mutator enzymes for the excision repair of 8-hydroxyguanine. DNA polymorphisms in human MMH/OGG1 gene were newly identified and analyzed to examine a possible association with lung-cancer risk by a population-based study. Polymorphic allele 3 in hMMH/OGG1 exon 1 was significantly prevalent among Japanese patients with adenocarcinoma of the lung [odds ratio (OR): 3.152, 95% confidence interval (CI): 1.266-7.845], indicating that the excision repair of 8-hydroxyguanine may play a role in predisposition to lung cancer.

Prenatal identification of mos 45,X/46,X,+mar in a normal male baby by cytogenetic and molecular analysis

We report a case of mos 45,X/46,X,+mar, diagnosed prenatally by amniocentesis, whose physical examination, including external and internal organs, along with serum testosterone values were normal five years after delivery. The mosaic karyotype was seen in 146 of 240 cells examined (amniotic fluid cells, 110/65; placental chorionic villi: 5/4; cord blood, 21/81; cultured skin fibroblasts, 10/90) from 386 metaphases, and the marker chromosome appeared as a small non-fluorescent acrocentric chromosome. All autosomes appeared normal, and no normal Y chromosome could be demonstrated. Analysis of 26 Y-chromosome loci by molecular techniques such as PCR, Southern analysis using multiple Y-specific DNA probes, and Hae III restriction endonuclease assessment of male-specific repeated DNA in the heterochromatic region of the Y chromosome, and fluorescence in situ hybridization (FISH), revealed the marker was derived from a Y chromosome including p terminal to q11.23, and paracentric inversion in the remaining Y long arm. The formation of testes can be considered as existence of SRY (sex-determining region of Y) as a testis-determining factor. The present report illustrates the importance of FISH and molecular techniques as a complement to cytogenetic methods for accurate identification and characterization of chromosome rearrangements in prenatal diagnosis.

Seminoma in a postmenopausal woman with a Y;15 translocation in peripheral blood lymphocytes and a t(Y;15)/45,X Turner mosaic pattern in skin fibroblasts

We report an unusual case of a 55 year old Japanese woman with a seminoma but relatively normal menses. The patient was a phenotypic female with late onset menarche (18 years of age), who was amenorrhoeic for the first year, followed by menses of one to three days' slight flow with dysmenorrhoea, but an otherwise normal menstrual history. A typical seminoma was removed from the left adnexal region and an immature testis was identified separately as an associated right adnexal mass. Repeated karyotypic studies on peripheral blood lymphocyte cultures showed only 46,X,-Y,t(Y;15)(q12;p13). Cytogenetic examination of the patient's younger brother, who had fathered three healthy children, showed an identical karyotype. Mosaicism of 46,X,-Y,t(Y;15)(q12;p13)/45,X cell lines was found in skin samples from the patient's elbow and genital regions, although there were no clinical stigmata of Turner syndrome. An androgen receptor binding assay of cultured genital skin fibroblasts was negative. Molecular analysis using Southern blot hybridisation, PCR, and direct DNA sequencing showed that neither the patient nor her brother had a detectable deletion or other abnormalities of Y chromosome sequences, including the SRY (sex determining region of the Y chromosome) gene sequence. These findings suggest that Turner mosaicism of the 45,X cell line may have contributed to this atypical presentation in an XY female, although we cannot exclude abnormalities of other genes related to sex differentiation.

Polymerase chain reaction analysis of the Y chromosome long arm in azoospermic patients: lack of the Y chromosome recognition motif (YRRM1) gene

We analyzed DNA from a patient with azoospermia whose Y chromosome was cytogenetically normal. A total of 16 loci on the Y chromosome long arm were examined: 15 loci between DYS7E and DYZ1, and the Y chromosome RNA recognition motif (YRRM1) locus, a candidate gene for the azoospermic factor AZF. We did not detect the YRRM1 gene in this patient. This finding supports the theory that YRRM1 is an essential gene for spermatogenesis.

Founder-haplotype analysis in Fukuyama-type congenital muscular dystrophy (FCMD)

Fukuyama-type congenital muscular dystrophy (FCMD) is an autosomal recessive, severe muscular dystrophy associated with brain anomalies. After our initial mapping of the FCMD locus to 9q31-33, we performed linkage disequilibrium analysis, which led us to suspect that the FCMD gene lay within a region of less than 100 kb containing D9S2107. In the present study, we developed two new microsatellites (D9S2170 and D9S2171) in close vicinity to D9S2107 and examined haplotypes of FCMD chromosomes by using four markers (cen-D9S2105-D9S2170-D9S2171-D9S2107-tel). As 82% of the FCMD chromosomes that we examined shared the founder haplotype (138-192-147-183) and 94% of the FCMD patients in our panel carried founder haplotypes on one or both chromosomes, the data supported the hypothesis of a single founder of this disease in the Japanese population. Eight haplotypes different from the founder's were observed in FCMD chromosomes, indicating that eight different FCMD mutations in addition to the founder's have occurred in Japan. Moreover, we have detected several historical recombinations that have disrupted the founder haplotype at D9S2105 or D9S2170 and conclude that the FCMD gene is probably located just centromeric to D9S2170.

Fibrinogenolytic activity of a novel trypsin-like enzyme found in human airway

Previously we isolated a new trypsin-like enzyme designated human airway trypsin-like protease (HAT) from human sputum. In this study, we examined in vitro whether HAT was related to the prevention of fibrin deposition in the airway lumen by cleaving fibrinogen. In mucoid sputum samples from patients with chronic airway diseases, the concentration of fibrinogen, as measured by ELISA, was in the range of 2-20 micrograms/ml, and trypsin-like activity, as measured by spectrofluorometry was in the range of 10-50 milliunits (mU)/ml. We showed by gel filtration that the trypsin-like activity of mucoid sputum was mainly due to HAT. We examined the effects of HAT on human fibrinogen at pH 7.4 and 8.6. Fibrinogen was used at concentrations of 4-2,000 micrograms/ml and HAT purified from sputum at concentrations of 0.6-10 mU/ml. As shown by SDS-polyacrylamide gel electrophoresis, HAT cleaved fibrinogen, especially its alpha-chain, regardless of the concentration of fibrinogen. Pretreatment of fibrinogen with HAT resulted in a decrease or complete loss of its thrombin-induced clotting capacity, depending on the duration of pretreatment with HAT and the concentration of HAT. From these results we postulated that HAT may participate in the anticoagulation process within the airway, especially at the level of the mucous membrane, by cleaving fibrinogen transported from the blood stream.