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Centre for Cellular and Molecular Biology (S.R., K.T., D.S.R., L.S.), Hyderabad 500 007, India; Institute of Reproductive Medicine (N.J.G., B.C.), Salt Lake, Kolkata 700 091, India; Division of Human Genetics (N.L., S.R.), St. Johns Medical College, Bangalore 560 034, India; Department of Genetics, Postgraduate Institute of Basic Medical Sciences (R.G.N., V.K., S.T.S., P.M.G.), University of Madras, Chennai 600 113, India; and KMC Life Science Centre (P.M.G.), Manipal Academy of Higher Education, Manipal 576 104, India
Address all correspondence and requests for reprints to: Dr. K. Thangaraj and Dr. Lalji Singh, Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India. E-mail: thangs@ccmb.res.in and lalji{at}ccmb.res.in.
| Abstract |
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Objective: The objective of this study is to map the chromosomal locus responsible for an unexplained sex-reversed phenotype.
Design: The study implemented a genome-wide scan using families with multiple sex-reversed individuals.
Setting: The patients, along with the family members, were selected from different hospitals/reproductive centers.
Participants: Sex-reversed individuals and their siblings and parents participated in the study.
Main Outcome Measures: Identification of the chromosomal locus responsible for sex reversal in these families and sequence analysis of candidate genes were the main outcome measures.
Results: Parametric linkage analysis revealed a maximum two-point LOD score of 5.70 with marker DXS991 (Xp11.21) and 4.57 with marker DXS1039 (Xp11.23-Xp11.22), and a multipoint LOD score of 5.77 with marker DXS991 and 5.22 with marker DXS1039. The two markers (DXS991 and DXS1039) with highest LOD score span approximately 3.41 cM (75.7979.2 cM) on the short arm of the X-chromosome.
Conclusion: Our findings provide evidence for a major susceptibility locus for sex reversal/gonadal dysgenesis on the short arm of the X-chromosome (Xp11.21-11.23). Furthermore, molecular exploration of the expression of candidate genes in the embryonic gonad/gonadal ridge will help in the identification of the underlying gene for sex reversal.
| Introduction |
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Despite the identification of the above genes, SRY was still the major sex-determining gene, and it was thought that the presence of SRY was mandatory for the male phenotype. However, the absence of SRY and apparently all other Y-chromosomal sequences in a substantial number of XX males and in most true hermaphrodites (9), and its presence in the majority of XY females who have no detectable SRY mutations (10), cannot be explained satisfactorily on the basis that the mere presence of SRY determines maleness. Evidence for an X-specific gene involved in sex determination was first postulated on the basis of a family with 46,XY gonadal dysgenesis (11). Affara (12) also suggested the presence of at least one additional key gene on the X-chromosome, downstream to SRY in the human sex-determining pathway. Furthermore, in certain reptiles (crocodilians and turtles), the incubation temperature of the egg determines the sex (13). These facts strongly suggest that certain gene(s) responsible for the differentiation of testes and ovary must be present in all the embryos. Thus determination, development, and differentiation of mammalian testes and ovaries from an embryonic bipotential gonad are controlled by a number of key genes interacting in an as yet poorly defined pathway (14).
Genes involved in sex determination have been identified mainly by deletion/duplication or translocation mapping in the cases of sex reversal/ambiguous sex. The fortuitous finding of chromosomal rearrangements in association with a sex-reversed phenotype has led to the isolation of the SRY and SOX9 genes (2, 3). Duplication of the distal Xp region resulted in the identification of DAX1 (6) and deletion studies resulted in the isolation of DMRT1/2/3 (15) and WT1 (16) from the short arms of chromosomes 9 and 11, respectively. The orphan nuclear receptor, SF1, was identified by targeted disruption of the Ftz-F1 gene in mice (17, 18).
Linkage studies to identify sex-determining genes are hampered by variation of the phenotypes in the affected families and the relative rarity of multigenerational pedigrees with several affected cases. Although many studies have reported familial cases of 46,XY gonadal dysgenesis (19, 20, 21), to our knowledge only two linkage studies for gonadal dysgenesis/sex reversal have been attempted thus far, of which one suggested linkage to chromosome 5 and the other also suggested involvement of an autosomal gene but could not establish strong linkage (22, 23). Therefore we have undertaken a genome-wide scan on nine familial cases of 46,XY sex reversal, which could not be explained by mutations in any of the known sex-determining genes, to search for additional chromosomal region(s) linked with sex reversal/gonadal dysgenesis.
| Subjects and Methods |
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A total of 15 46,XY sex reversal families with gonadal dysgenesis were collected from different regions of India through our collaborating organizations. A proper phenotype (Table 1
) was set for the selection of the familial cases. Five families with varying phenotype among siblings were excluded from the study to avoid locus heterogeneity. After molecular genetic analysis, nine families were finally selected for linkage analysis, which comprised a total of 58 individuals, including 17 patients and 35 informative individuals. Each family included in the linkage study had both parents with at least two informative individuals and no history of consanguinity (Fig. 1
). All the participants donated blood samples with informed written consent. The study was approved by the institutional ethical committee.
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Serum levels of testosterone, 17-hydroxyprogesterone, FSH, and LH for the probands and the affected siblings were measured by RIAs.
Cytogenetic analysis
Peripheral blood lymphocyte cultures for all the family members were set up in duplicate in 5-ml culture vials using RPMI media supplemented with 10% fetal calf serum. Cells were grown in the presence of penicillin/streptomycin/gentamycin. Phytohemagglutinin was added to stimulate cell division. Dividing cells were arrested at metaphase stage with colchicin and fixed in methanol/acetic acid (3:1). Fixed cells were dropped onto glass slides and allowed to air-dry. Chromosomes were G-banded by treating the preparations with trypsin followed by staining with giemsa.
Histological studies
Histological studies were done for 11 of 17 patients because the others were below puberty. Gonadal tissue of the proband and other affected individuals was fixed using 10% buffered neutral formalin solution at room temperature for 7 d. Tissue was dehydrated with isopropanol, cleared with xyline at room temperature, and impregnated with paraffin wax at 58 C. Tissue embedded in paraffin wax was cut into 4-µm-thick sections using LeicaRM2135 microtome (Leica, Bensheim, Germany). The sections were taken directly on egg albumin-coated glass slides and kept at 60 C for 1 h. Slides were dewaxed with xyline and stained with hematoxylin followed by eosin. After staining, slides were mounted with dipthyline xyline and observed using Axioplan imaging system (Zeiss, Oberkochen, Germany), and images were captured at different magnifications.
PCR and sequencing of the known sex-determining genes
DNA was extracted from peripheral blood samples of all the participants using protocol described elsewhere (24). PCR primers for SRY and DAX1 were as used in earlier studies (25, 26), whereas primers for SOX9, SF1, and WT1, including the splice junctions (Supplemental Table S1, published as supplemental data on The Endocrine Societys Journals Online web site at http://jcem.endojournals.org), were designed using GeneTool software and synthesized using 394 DNA/RNA oligosynthesizer (Applied Biosystems, Foster City. CA). Exonic regions of the above genes were amplified and sequenced using dideoxy chain terminator cycle sequencing protocol (BigDye) and 3700 DNA analyzer (Applied Biosystems) (27).
Sequencing of the candidate genes
The candidate genes were selected on the basis of their expression pattern and the putative role as transcription factors. We sequenced the coding regions of WD repeat domain 13 (WDR13), melanoma antigen family D, 1 (MAGED1), Kruppel-like factor 8 (KLF8), and zinc finger protein 157 (ZNF157) genes. The primers for sequencing the aforementioned genes were designed to include the splice junctions (Supplemental Table S1). Synthesis of primers and the sequencing methods used were as mentioned above.
Genotyping
In the first phase of genotyping, 437 Microsatellite markers (Linkage Mapping Set, MD10, V 2.5; Applied Biosystems), spanning the entire human genome, were amplified individually in 10 µl PCR. In the second phase of genotyping, 11 high-density markers (HDM) were amplified and genotyped. In the third phase of analysis, 26 micro-density markers (MDM) were amplified to check for recombination in the region of interest. For each linkage panel, amplicons were pooled in different ratios, depending upon the fluorescent label, and analyzed on ABI3730 DNA Analyzer (Applied Biosystems) using LIZ 500 as size-standard. The raw data were further analyzed using GeneMapper software. Same markers were amplified for control DNA (CEPH, 1347-02) and conversion table made for all the markers to avoid errors in sizing alleles, arising due to run-to-run differences.
Statistical analysis
In each phase of linkage mapping, two-point LOD scores were calculated using FASTLNIK package (28), assuming autosomal dominant model of inheritance for autosomal markers and X-linked recessive mode of inheritance for the X-linked markers. Multipoint linkage analysis was done for the markers in the critical region of the X-chromosome. The abnormality was assumed to have full penetrance and an allele frequency of 0.001. Simulation studies were done using MEGA2 (29) and SIMULATE (30) programs.
| Results and Discussion |
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The absence of additional phenotypic features associated with Campomelic dysplasia, Denys-Drash, and Frasier syndrome excluded the involvement of the SOX9, DAX1, WT1, and SF1 genes in all these families. Patient samples from each of the 10 families were subjected to sequencing of the known sex-determining genes (SRY, SOX9, DAX1, WT1, and SF1) to see whether the abnormality could be attributed to mutation in any of these genes. This analysis revealed that one family carried a partial deletion of the SRY gene, but detected no mutations in the remaining nine families. Each of the nine families included in the linkage study consisted of both parents with at least two informative individuals, and had no history of consanguinity (Fig. 1
). Despite the apparent X-linked mode of inheritance of the sex-reversed phenotype in all the families, a genome-wide scan was performed to explore the possibilities of linkage to chromosomal region(s) other than the X-chromosome.
In the first phase of the analysis, a genome-wide scan was performed with 400 low-density short tandem repeat markers (average heterozygosity 0.79) spaced at an average resolution of 9.22 cM and spanning the whole human genome (Linkage Mapping Set MD10, V 2.5; Applied Biosystems). All the pedigrees were consistent with X-linked recessive mode of inheritance, although a sex-limited autosomal dominant mode could not be excluded. We performed parametric linkage analysis because of the higher power of parametric methods to detect linkage than nonparametric ones. For parametric analysis with the autosomal markers, autosomal dominant model was assumed. For all the X-specific markers, an X-linked recessive model of inheritance was assumed. The disease was assumed to have full penetrance with an allele frequency of 0.001. Two-point analysis was performed for all the markers using the FASTLINK package (28), but multipoint linkage analysis was carried out only for the markers in the critical region of the X-chromosome. Although many regions on different chromosomes yielded a LOD score of more than 1.0 (Table 2
), a maximum two-point LOD score of 5.70 (
consistent at 0.00 for all of the nine families) and multipoint LOD score of 5.77 (
consistent at 0.01 for all of the nine families) was observed with the marker DXS991 on the X-chromosome (Tables 3
and 4
and Figs. 2
and 3
). All the families analyzed showed consistent linkage with marker DXS991 (Fig. 1
). This narrowed the region of interest to approximately 30 cM on the short arm of the X-chromosome.
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consistent at 0.00 for all of the nine families) (Table 3
consistent at 0.00 for all of the nine families) with marker DXS1039, just adjacent to DXS991 (Table 4
consistent at 0.00 in all of the nine families) and multipoint LOD score of 4.51 (
consistent at 0.10 in all of the nine families) was observed with DXS1216 also, a marker next to DXS1039. Linkage with DXS1039 was observed in seven families; the remaining two families were uninformative because of homozygosity in the mother (Fig 1
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To estimate the probability of getting a LOD score of 5.77 by chance, simulation studies with 1000 unlinked replicates were conducted using the MEGA2 (29) and SIMULATE (30) software packages. The LOD score in the simulation studies never exceeded 2.5 (threshold LOD score) at P = 0.05. The statistical analysis was repeated with different marker allele frequencies (including an increase of the minor allele and decrease of the major allele frequencies), to estimate their effect on our results. However, the results were robust to variation in marker allele frequencies.
Interestingly, no previous study has reported the involvement of Xp11.21-11.23 in sex reversal. Because the mutation(s) in the underlying gene in the present cases resulted in gonadal dysgenesis, this gene must have a role in testis differentiation/sex determination. The geographical distribution of the families used in this study does not indicate the common ancestry and hence founder effect. According to the X-chromosome gene annotation available in human genome database, at least 53 genes map to Xp11.21-11.23. Several of the genes involved in gonadal development described to date are transcription factors, and hence the ZNF family genes and some members of the SSX, MAGE, GAGE, and ZNF gene families, which are transcription factors, may be the likely candidates for sex determination. An earlier in silico study involving the search of the human genome for inverted repeat palindromes revealed many genes in the above region of the X-chromosome, of which some members of SSX, GAGE, and MAGE gene families were found to be expressed in testis (31). Our earlier study on screening of a human testis cDNA library with a Bkm (Banded Krait Minor satellite DNA) probe resulted in the isolation of a highly conserved WDR13 gene from Xp11.23. This gene is another potential candidate for sex determination, given high activity of its promoter in fetal and adult testes (32). Xp11.23 and the region distal to this are conserved in monotremes, marsupials, and placental mammals and were translocated from autosomes (33). Given that mammalian sex chromosomes evolved as specialized chromosome pair for sex determination, the evolutionary history also supports the presence of some sex-determining gene(s) in this region of the X-chromosome.
DNA sequence analysis of four candidate genes (WDR13, MAGED1, KLF8, ZNF157) in XY females did not reveal any mutation in any of these genes. Because the sex of the embryo is determined at the very early embryonic stages, the sex-determining genes must express during the early stages of gonad differentiation, the expression of which may reduce or cease all together in adult testes. The expression of a gene in adult testis doesnt signify its expression in the indifferent gonad as well. The lack of the information about the expression of the genes in the candidate region in the indifferent gonad is the major complicating factor in the selection of the candidate genes more precisely and hence finding the underlying gene. Therefore, it is not sure whether the genes sequenced were really the top candidate genes for the sex-reversed phenotype (46,XY female). This may be one of the reasons why sequencing of four candidate genes did not reveal any mutation in the cases. To select the candidate genes more precisely, the information regarding the expression of these genes in the indifferent gonad is must. Availability of such information in databases would be immensely useful for selecting the right candidate gene(s).
Successful mapping of gonadal dysgenesis/sex reversal on the X-chromosome in the present study will fuel the search for further sex-determination genes and encourage such studies to explore the full sex-determination pathway. Mapping of the sex-reversed phenotype to the same locus in all the families studied reflects the importance of careful selection of the cases. This study is the first of its kind with multiple pedigrees, and further studies are needed to replicate these results and narrow down the interval harboring the underlying gene. With more information on the expression pattern of these genes in the embryonic tissues such as gonadal ridge, the selection of the candidate genes would become more accurate and help in screening of the best candidates at the earliest time. An additional factor that needs to be considered is the dosage of the genes in the interval, as illustrated by the duplication of DAX1 gene resulting in sex reversal (6). Identification of sex-determining gene(s) and establishment of the full pathway will help not only in appropriate management of cases of sex reversal/ambiguous sex, but also in understanding the molecular aspects of organogenesis.
| Acknowledgments |
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| Footnotes |
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Disclosure Summary: All authors have nothing to declare.
First Published Online July 25, 2006
1 S.R. and K.T. contributed equally. ![]()
Abbreviations: HDM, High-density marker; MDM, micro-density marker; SRY, sex-determining region on Y-chromosome.
Received May 4, 2006.
Accepted July 19, 2006.
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