Chromosome Xp11 Research Articles

IPEX with Normal FOXP3 Gene and Diminished Expression

RATIONALE: Immunodysregulation, polyendocrinopathy, enteropathy syndrome (IPEX) is a rare disorder that results from mutations of the forkhead helix transcription factor FOXP3 gene on chromosome Xp11.23. FOXP3 is expressed by CD4+ CD+25 regulatory T cells, and has been identified as a vital regulator of T cell development and function. Nonfunctional FOXP3 allows the hyperactivation of T cells, resulting in dermatitis, enteropathy, type 1 diabetes, thyroiditis, hemolytic anemia, and thrombocytopenia.

Validation of mRNA/EST-based gene predictions in human Xp11.4 revealed differences to the organization of the orthologous mouse locus

Careful manual annotation of the human reference sequence provides a solid basis for the identification of disease-associated genes. Toward this end, we focused on a medically relevant 2.6-Mb region of the human chromosome Xp11.4 between markers DXS9851 and DXS9751 and identified 16 transcription units according to the Vertebrate Genome Annotation (Vega) rules. In order to validate these annotations, we performed a comprehensive RT-PCR expression analysis and a human-mouse comparison. This revealed, despite the high overall genomic conservation of the region, remarkable differences of the gene content between human and mouse. Whereas 12 of 16 annotations were confirmed by RT-PCR in human tissues, for only seven genes mouse orthologs could be identified and found to be expressed. This indicates that a comprehensive and experimentally supported annotation effort of the human genome simultaneously highlights regions with striking differences in gene organization to other species and may indicate evolutionary events specific to the human lineage demanding further functional analyses.

Three Kinships with ALAS2 P520L Mutations, Two in Association with Severe Iron Overload, and One with Sideroblastic Anemia and Severe Iron Overload.

Aminolevulinate synthase 2 (ALAS2) is an erythroid-expressed gene located on chromosome Xp11.21. Mutations in ALAS2 have been shown to be associated with sideroblastic anemia. We have identified a novel mutation in ALAS2, P520L, in three kinships. The P520L mutation was not found in 316 white male control subjects. The proline in this position is highly conserved across species from humans to zebrafish.In the C kinship, the P520L mutation was first identified in a white man who presented with severe iron overload at an early age and was a HFE C282Y homozygote. Genetic analyses of members of the C kinship suggest that the presence of P520L alone in hemizygous males, or simple heterozygosity in females, is not associated with anemia or iron overload. Females heterozygous for both HFE C282Y and ALAS2 P520L also had normal ferritin levels. Only subjects homozygous for HFE C282Y and hemizygous or heterozygous for ALAS2 P520L had severe iron overload. Sequencing studies revealed that the propositus did not have missense mutations in HAMP, HJV, FPN1, ABC7, IL6, or RAG1.In the H kinship, the propositus was a white woman with severe iron overload who was heterozygous for ALAS2 P520L; she had a wildtype HFE genotype. The pedigree of the H kinship identified 5 additional females who were heterozygous for the P520L ALAS2 mutation. Only the propositus had iron overload and none of the subjects with P520L had sideroblastic anemia. The propositus did not have missense mutations in FPN1, HAMP, HJV, TFR2, B2M, IRP2, ABC7, or SFT. We speculate that the propositus in the H kinship has a mutation in a currently unknown gene that contributes to her severe iron overload. In the S kinship, the P520L mutation was identified in a white man with sideroblastic anemia and severe iron overload. The patient had a second mutation in ALAS2, R560H, a mutation previously described in two brothers with sideroblastic anemia of variable penetrance (Blood 100:4236–4238, 2002). It is not possible to determine the effect of the P520L mutation on the penetrance of the R560H-associated sideroblastic anemia and iron overload.We conclude that the ALAS2 P520L occurs at a very low allele frequency in the white population. The present observations also suggest that there is no distinctive phenotype associated with the P520L mutation alone, but that P520L may act as a modifier of iron overload in the presence of HFE homozygosity, other missense mutations of ALAS2, or mutations of uncharacterized iron regulatory genes.

Evidence for de novo imprinted X-chromosome inactivation independent of meiotic inactivation in mice

In mammals, one of the two X chromosomes is inactivated in females to enable dosage compensation for X-linked gene products. In rodents and marsupials, only the X chromosome of paternal origin (Xp) is silenced during early embryogenesis. This could be due to a carry-over effect of the X chromosome's passage through the male germ line, where it becomes transiently silenced together with the Y chromosome, during meiotic sex chromosome inactivation (MSCI). Here we show that Xist (X inactive specific transcript) transgenes, located on autosomes, do not undergo MSCI in the male germ line of mice and yet can induce imprinted cis-inactivation when paternally inherited, with identical kinetics to the Xp chromosome. This suggests that MSCI is not necessary for imprinted X-chromosome inactivation in mice. We also show that the Xp is transcribed, like autosomes, at zygotic gene activation rather than being 'pre-inactivated'. We propose that expression of the paternal Xist gene at zygotic gene activation is sufficient to trigger cis-inactivation of the X chromosome, or of an autosome carrying a Xist transgene.

Interspecies synteny mapping identifies a quantitative trait locus for bone mineral density on human chromosome Xp22

Bone mineral density (BMD) is a complex trait with a strong genetic component and an important predictor of osteoporotic fracture risk. Here we report the use of a cross-species strategy to identify genes that regulate BMD, proceeding from quantitative trait mapping in mice to association mapping of the syntenic region in the human genome. We identified a quantitative trait locus (QTL) on the mouse X-chromosome for post-maturity change in spine BMD in a cross of SAMP6 and AKR/J mice and conducted association mapping of the syntenic region on human chromosome Xp22. We studied 76 single nucleotide polymorphisms (SNP) from the human region in two sets of DNA pools prepared from individuals with lumbar spine-BMD (LS-BMD) values falling into the top and bottom 13th percentiles of a population-based study of 3100 post-menopausal women. This procedure identified a region of significant association for two adjacent SNP (rs234494 and rs234495) within the Xp22 locus (P<0.001). Individual genotyping for rs234494 in the BMD pools confirmed the presence of an association for alleles (P=0.018) and genotypes (P=0.008). Analysis of rs234494 and rs234495 in 1053 women derived from the same population who were not selected for BMD values showed an association with LS-BMD for rs234495 (P=0.01) and for haplotypes defined by both SNP (P=0.002). Our study illustrates that interspecies synteny can be used to identify and refine QTL for complex traits and represents the first example where a human QTL for BMD regulation has been mapped using this approach.

Dent's disease

Dent's disease is a renal tubular disorder characterized by manifestations of proximal tubule dysfunction, including low-molecular-weight proteinuria, hypercalciuria, nephrolithiasis, nephrocalcinosis, and progressive renal failure. These features are generally found in males only, and may be present in early childhood, whereas female carriers may show a milder phenotype. Prevalence is unknown; the disorder has been reported in around 250 families to date. Complications such as rickets or osteomalacia may occur. The disease is caused by mutations in either the CLCN5 (Dent disease 1) or OCRL1 (Dent disease 2) genes that are located on chromosome Xp11.22 and Xq25, respectively. CLCN5 encodes the electrogenic Cl-/H+ exchanger ClC-5, which belongs to the CLC family of Cl- channels/transporters. OCRL1 encodes a phosphatidylinositol bisphosphate (PIP2) 5-phosphatase and mutations are also associated with Lowe Syndrome. The phenotype of Dent's disease is explained by the predominant expression of ClC-5 in the proximal tubule segments of the kidney. No genotype-phenotype correlation has been described thus far, and there is considerable intra-familial variability in disease severity. A few patients with Dent's disease do not harbour mutations in CLCN5 and OCRL1, pointing to the involvement of other genes. Diagnosis is based on the presence of all three of the following criteria: low-molecular-weight proteinuria, hypercalciuria and at least one of the following: nephrocalcinosis, kidney stones, hematuria, hypophosphatemia or renal insufficiency. Molecular genetic testing confirms the diagnosis. The differential diagnosis includes other causes of generalized dysfunction of the proximal tubules (renal Fanconi syndrome), hereditary, acquired, or caused by exogenous substances. Antenatal diagnosis and pre-implantation genetic testing is not advised. The care of patients with Dent's disease is supportive, focusing on the treatment of hypercalciuria and the prevention of nephrolithiasis. The vital prognosis is good in the majority of patients. Progression to end-stage renal failure occurs between the 3rd and 5th decades of life in 30-80% of affected males.

Long Polymerase Chain Reaction-Based Fluorescence in Situ Hybridization Analysis of Female Carriers of X-Linked Chronic Granulomatous Disease Deletions

Chronic granulomatous disease (CGD) is a rare inherited disorder in which antimicrobial activity of phagocytes is impaired due to the lack of reactive oxygen species, or oxidative burst, produced by NADPH oxidase. The X-linked form of CGD, representing approximately 70% of all cases, is caused by mutations in the cytochrome b beta subunit (CYBB) gene, which maps to chromosome Xp21.1. CYBB encodes the gp91-phox protein, a necessary component in the NADPH oxidase pathway. A wide variety of mutations have been identified in X-linked CGD patients, all of which lead to deletion of the functional protein and no oxidative burst activity. The mutations vary from single nucleotide substitutions to deletions of the entire gene. In this article, we report a mutation detection method for probands of female relatives at risk for carrier status of large deletions of the CYBB gene. Through fluorescent in situ hybridization of metaphase chromosomes, we were able to consistently distinguish carriers from noncarriers using polymerase chain reaction-derived, labeled DNA specific for exons 2 to 13 of the CYBB region at Xp21.1.

Imprinted X inactivation and reprogramming in the preimplantation mouse embryo

X chromosome inactivation is a developmentally regulated process that causes one of the two X chromosomes in normal female mammals to become transcriptionally silenced, thus equalizing the expression of X-linked genes between the sexes. Such dosage compensation depends upon dynamic genetic and epigenetic events occurring very early in development. X inactivation is controlled by an X inactivation centre that is associated with the expression of non-coding RNAs required for the silencing. Also associated with the inactive X are repressive histone modifications and polycomb protein-mediated states, which are progressively acquired during the inactivation process. In mouse, two forms of X inactivation have been described. Random X inactivation happens in the derivatives of the inner cell mass (ICM) giving rise to embryos where the maternally inherited X(Xm) is inactive in some cells and the paternally derived X (Xp) is inactive in others. Random X inactivation occurs around the time of implantation. Imprinted X inactivation, the preferential inactivation of the Xp chromosome, occurs earlier and, although there has been some debate as to the precise timing of initiation of this event, is apparent in all cells early in preimplantation development, then is subsequently confined to the cells of the extraembryonic lineages. A picture is emerging whereby initial epigenetic asymmetry between the two parental X chromosomes is reprogrammed in a lineage specific manner resulting in a switch from imprinted to random inactivation in embryonic derivatives. Neither the underlying reason nor the full extent of these early lineage specific epigenetic changes is known, but they may be correlated with more genome-wide reprogramming events essential for normal development.

CLCN5 mutation (R347X) associated with hypokalaemic metabolic alkalosis in a Turkish child: an unusual presentation of Dent's disease

Dent’s disease, an X-linked recessive tubular disorder, is characterized by low molecular weight proteinuria (LMWP) and nephrolithiasis associated with nephrocalcinosis and hypercalciuria. It is due to mutations that inactivate the renal voltage-gated chloride channel ClC-5 [1,2], which is encoded by a gene (CLCN5) located on chromosome Xp11.22. It is possible, however, that causative mutations were not identified in some patients with Dent’s disease [3–6]. Renal acidification abnormalities have not been a consistent feature of the phenotype, probably being secondary to long-standing hypercalciuria and nephrocalcinosis. Hypokalaemic metabolic alkalosis, however, has not been reported previously in Dent’s disease. Inherited disorders that manifest hypokalaemic metabolic alkalosis, such as the Bartter–Gitelman syndrome or the hyperprostaglandin E syndrome (also referred to as antenatal Bartter’s syndrome), are caused by the malfunction of renal tubular electrolyte transporters or ion channels. The hyperprostaglandin E syndrome is linked to the dysfunction of the sodium– potassium–chloride co-transporter (NKCC2) [7] or the renal outer medullary potassium channel (ROMK) [8]. The cardinal features of the syndrome are its antenatal onset—with polyhydramnios due to fetal polyuria, isothenuria and medullary nephrocalcinosis. When associated with sensorineural deafness or autosomal dominant hypocalcaemia, the hyperprostaglandin E syndrome is due to mutations in barttin, a b subunit of voltage-gated chloride channels [9], and the calcium-sensing receptor CaSR [10]. Bartter–Gitelman syndrome is linked to mutations in the basolateral chloride channel (ClC-Kb) [11] or in the sodium– chloride co-transporter (NCCT) [12]. The course of this disease is usually milder, mimicking chronic use of thiazides. ROMK, NKCC2 and NCCT mutations usually have uniform clinical presentations, whereas mutations in CLCNKB, encoding ClC-Kb, occasionally lead to phenotypic overlaps with the ROMK/ NKCC2 cohort. This study describes the first case of Dent’s disease due to a loss-of-function mutation in the CLCN5 gene, R347X, associated with a Bartter-like syndrome that is characterized by hypokalaemic metabolic alkalosis and secondary hyper-reninaemic hyperaldosteronism.

Functional disomy of Xp: Prenatal findings and postnatal outcome

We report on trisomy of the short arm of the X chromosome (Xp11.2 --> pter) due to a de novo unbalanced X;13 translocation diagnosed prenatally in a female fetus. Amniocentesis was performed at 20-weeks' gestation following ultrasound finding of a Dandy-Walker malformation. The trisomy of Xp11.2 --> pter was confirmed with fluorescence in situ hybridization (FISH), using an X chromosome painting probe and telomeric FISH probes specific for the short arm of chromosome X. The karyotype was defined as 46,XX,der(13)t(X;13)(p11.2;p11.2). Molecular analysis suggested that the extra Xp material was of paternal origin. FISH analysis with an XIST probe showed that the derivative chromosome 13 did not include the XIST locus at the X-inactivation center (XIC). A complex phenotype was seen at birth including macrosomia, facial dysmorphism with preauricular tag, congenital heart defects, and structural brain malformations. Because the derivative chromosome was not subject to X inactivation, functional disomy of Xp11.2 --> pter most likely accounts for the abnormal phenotype in this patient.

Expression of receptor tyrosine kinases epidermal growth factor receptor and HER‐2/neu in synovial sarcoma

Synovial sarcomas are high-grade soft tissue neoplasms often characterized by a biphasic spindle and epithelioid cell morphology. The majority of synovial sarcomas harbor a specific chromosomal translocation in which the proximal portion of the SYT gene at chromosome 18q11 is fused to the distal portion of one of several duplicated SSX genes (most notably SSX1 and SSX2) at chromosome Xp11. SYT/SSX1 translocations are seen in nearly three times as many synovial sarcomas as SYT/SSX2 translocations. Although the SYT/SSX2 fusion is usually associated with the monophasic disease pattern, the SYT/SSX1 fusion is present in tumors with biphasic or monophasic patterns. The SYT/SSX1 fusion gene is associated with more aggressive tumor growth and poor outcome. Despite advances in the therapy of local disease, distant metastasis remains the predominant cause of death. Accordingly, there is a need for alternate therapies, such as those recently developed against the receptor tyrosine kinases, such as epidermal growth factor receptor (EGFR) and HER-2/neu. Archival specimens of synovial sarcoma (n=38) representing 30 patients were assessed for EGFR and HER-2/neu protein expression by standard immunohistochemical techniques. To validate the immunohistochemistry results, quantitative real-time polymerase chain reaction (Q-PCR) assays using either fresh and/or archival material was performed. The presence of gene amplification was determined by chromogenic in-situ hybridization. EGFR and HER-2/neu protein were detected by immunohistochemistry in 21 of 38 (55.3%) and 20 of 38 (52.6%) synovial specimens, respectively. EGFR immunoreactivity showed a granular and membranous pattern, whereas HER-2/neu immunoreactivity demonstrated only a membrane pattern. Coexpression was observed in 13 of 38 specimens (34.2%). HER-2/neu expression by immunohistochemistry in synovial sarcomas was restricted to tumors with the SYT/SSX1 translocations. Of 6 specimens with SSX2 translocation, none (0%) showed HER-2/neu immunoreactivity and 1 (17%) demonstrated EGFR expression. Q-PCR demonstrated the presence of mRNA for EGFR and HER-2/neu in 19 of 30 specimens (63.3%) and 22 of 30 specimens (73.3%), respectively. EGFR and HER-2/neu were expressed at low concentrations compared with the expression of glyceraldehyde 3-phosphate dehydrogenase (GAPDH). No evidence of gene amplification was observed. EGFR and HER-2/neu are expressed in the majority of patients with SYT/SSX1 synovial sarcomas, albeit at low levels. Treatment with tyrosine kinase inhibitors may represent appropriate alternate therapy for these patients.

The Evolving Concept of Renal Neoplasia: Impact of Emerging Molecular and Electron Microscopic Studies

The classification of renal tumors has evolved from one that initially encompassed only 2 types of tumors, i.e., clear and granular cell carcinomas, to the markedly expanded recent classification that incorporates new entities, some of which are primarily defined by specific molecular abnormalities. Despite these advances, a single tumor category, clear cell carcinoma, still incorporates the majority (∼70%) of renal tumors. It is, however, postulated that this single category is likely to encompass several different tumor types that are, at present, undifferentiated. Electron microscopic studies have been pivotal in defining the spectrum of oncocytoma–chromophobe renal cell carcinoma. Cytoplasmic eosinophilia found in some renal cell carcinomas currently classified as clear cell type is under intense study. Tumors that have recently emerged from this group include tumors with translocations involving chromosome Xp11.2, carcinomas associated with neuroblastoma and epithelioid angiomyolipoma. The spectrum of renal tumors seen in younger patients is wider than among older patients, with rare and unusual tumors being more likely seen in younger patients. The author concludes that although the routine application of electron microscopy to kidney tumor diagnosis may not be practical, systematic ultrastructural studies of these tumors may aid in the definition of new entities.

Chromosomal imbalances in sporadic neuroendocrine tumours of the thymus

Neuroendocrine (carcinoid) tumours of the thymus are rare neoplasms characterized by a highly malignant clinical behavior. Some of these tumors are associated with MEN1. In this study we evaluated 10 cases of sporadic thymic neuroendocrine tumours using immunohistochemistry and comparative genomic hybridization (CGH). All tumours showed a diffuse expression of neuron specific enolase (NSE) and synaptophysin. Chromosomal imbalances were detected in 8/10 cases, the most frequent gains were seen on chromosome Xp (3/10 cases), 7p, 7q, 11q, 12q, and 20q (2/10 each), losses were most frequently detected at 6q (5/10 each), 6p (3/10 each), 4q (3/10 each), 3p, 10q, 11q and 13 q (2/10 each). These CGH data show a degree of overlap with chromosomal imbalances commonly observed in advanced thymomas.

Glucocorticoids upregulate FOXP3 expression and regulatory T cells in asthma

T regulatory (T reg ) cells are characterized by expression of suppressive cytokines and the transcription factor FOXP3. They play a key role in balancing immune responses and maintain peripheral tolerance against antigens and allergens. The loss of peripheral tolerance against allergens causes diseases that can be therapeutically controlled with glucocorticoids. The present study investigates whether glucocorticoids affect the activity of T reg cells on the basis of FOXP3 and cytokine expression. CD4 + T cells from healthy donors and glucocorticoid-treated asthmatic patients were isolated, and expression of FOXP3, along with IL-10 and TGF-beta1, was determined. The effect of glucocorticoids on T reg cells was measured in vivo before and after GC treatment and in in vitro cultures. FOXP3 mRNA expression was significantly increased in asthmatic patients receiving inhaled glucocorticoid treatment, systemic glucocorticoid treatment, or both. FOXP3 tightly correlated with IL10 mRNA expression. No correlation of FOXP3 mRNA expression was observed in relation to a (GT)n microsatellite promoter polymorphism on chromosome Xp11.23 or total IgE level. The frequency of CD25 + memory CD4 + T cells and transient FOXP3 mRNA expression by CD4 + T cells significantly increased after systemic glucocorticoid treatment, whereas TGFB1 expression did not change. Furthermore, glucocorticoids induced IL10 and FOXP3 expression in short-term and long-term cultures in vitro. These findings demonstrate that glucocorticoid treatment is not only immunosuppressive and anti-inflammatory but also promotes or initiates differentiation toward T R 1 cells by a FOXP3-dependent mechanism. Strategies that convert transient glucocorticoid-induced T reg activity into a stable phenotype might improve allergy and asthma therapy.

Primary amenorrhea in a woman with a cryptic complex chromosome rearrangement involving the critical regions Xp11.2 and Xq24

To characterize a complex chromosome rearrangement (CCR) previously detected by G-banding in peripheral blood lymphocytes, as 46,X,-2,-11,-22,-X,+mar 1+mar2+mar3+mar4 in a patient with primary amenorrhea. Case report. University faculty of Medicine and hospital. A 36-year-old woman with primary amenorrhea. Fluorescence in situ hybridization (FISH). Use of commercially available M-FISH probe (24 colors simultaneously) and whole chromosome painting probes for chromosomes 2, 11, 22, and X to characterize the CCR. The use of conventional and multiple FISH allowed the redefinition of the CCR, showing a cryptic insertion of chromosome 11 in marker 3 previously suspected by M-FISH. The combination of G-banding and FISH data revealed that four chromosomes and seven breakpoints, including 2q21, 2q31, 11q22.1, 11q22.3, 22q13.3, Xp11.21, and Xq24, were implicated in this CCR. This report confirms the importance of a combination of G-banding and FISH (M-FISH and conventional FISH) techniques to characterize the de novo CCR. These techniques also were useful in defining two possible critical chromosome regions, Xp11.21 and Xq24, in which genes of potential interest for a primary amenorrhea could be located.

Genome-Wide Scan for Japanese Familial Intracranial Aneurysms

Genetic factors have an important role in the pathogenesis of intracranial aneurysm (IA). The results of previous studies have suggested several loci. From 29 IA families with > or =3 individuals affected by IA, we used nonparametric (model-free) methods for linkage analyses, using GENEHUNTER and Merlin software. Genome-wide linkage analyses revealed 3 regions on chromosomes 17cen (maximum nonparametric logarithm of the odds score [MNS] = 3.00, nominal P=0.001), 19q13 (MNS=2.15, nominal P=0.020), and Xp22 (MNS=2.16, nominal P=0.019). We tested 4 candidate genes in these regions: the microfibril-associated protein 4 gene (MFAP4) and the promoter polymorphism of the inducible nitric oxide synthase gene (NOS2A) on chromosome 17cen, the epsilon genotypes of the apolipoprotein E gene (APOE) on chromosome 19q13, and the angiotensin I converting enzyme 2 gene (ACE2) on chromosome Xp22. Associations of their polymorphisms with IA were evaluated by a case-control study (100 cases: 29 probands from IA families and 71 unrelated subjects with IAs, 100 unrelated control subjects [unaffected members with IAs and absence of family history of IAs]). However, the case-control study showed that none of the polymorphisms of the examined genes had associations with IA. A genome-wide scan in 29 Japanese families with a high degree of familial clustering revealed 1 suggestive linkage region on chromosome 17cen and 2 potentially interesting regions on chromosomes 19q13 and Xp22. These regions were consistent with previous findings in various populations.

Germ-line mutation of Foxn5 gene in mouse lineage

Amplified region (amplicon) around MLL gene is closely linked to the 11q23.3 commonly deleted region of neuroblastoma, which includes cancer-associated genes such as PHLDB1 (LL5A), BCL9L, FOXN5 (FOXR1), CBL, MFRP, and PVRL1 (Nectin) genes. FOXN6 (FOXR2) gene at human chromosome Xp11.21 is generated due to retrotransposition of ancestral Foxn5 gene during evolution. FOXN5 and FOXN6 orthologs share the common domain structure consisting of FN56 and Forhead-box (FOX) domains. Here, we identified and characterized mouse Foxn5 gene by using bioinformatics. Mouse Foxn5, consisting of six exons, was located within mouse genome sequences AC122428.4 and AC125129.5. Foxn5 locus at mouse chromosome 9B was synthenic to rat chromosome 8q22 and human chromosome 11q23.3. Mouse Foxn5 (180 aa) was C-terminally truncated compared with rat Foxn5 and human FOXN5. Mouse 'Foxn5' protein without FOX domain was generated due to a frame shift introduced by germ-line one-base deletion within exon 3. Mouse Foxn5 mRNA was expressed in embryonic germ cells and fertilized eggs. Germ-line mutation of Foxn5 gene in the mouse lineage might lead to divergent scenario of early embryogenesis between mouse and rat through the deregulation of Foxn5 target genes in mouse early embryos, and explain the difficulty in manipulation of rat embryonic stem (ES) cells based on the mouse equivalent system. This is the first report on identification and characterization of mouse Foxn5 gene as well as on species specific germ-line mutation of the Fox family gene.

Identification and characterization of human FOXN6, mouse Foxn6, and rat Foxn6 genes in silico

Forkhead-box (FOX) transcription factors are implicated in carcinogenesis through gene amplification, retroviral integration, or chromosomal translocation. FOXN1, FOXN2 (HTLF), FOXN3 (CHES1), FOXN4 and FOXN5 (FOXR1) constitute the FOXN family. Here, we identified and characterized human FOXN6 (FOXR2) and rodent Foxn6 (Foxr2) orthologs by using bioinformatics. Human FOXN6 gene was identified within human genome sequence RP11-167P23 (AL159987.19), mouse Foxn6 gene within mouse genome sequence RP23-180D16 (AL672293.14), and rat Foxn6 gene within rat genome sequence CH230-264B14 (AC106980.5). FOXN6, RRAGB (RAGB), and KLF8 genes were clustered at human chromosome Xp11.21. Foxn6, Rragb, and Klf8 genes were also clustered at mouse chromosome XF3 as well as at rat chromosome Xq14. Human FOXN6 mRNA was expressed in breast cancer cell line and primary breast cancer. Mouse Foxn6 mRNA was expressed in E9.5 embryo. Human FOXN6 (286 aa) showed 57.7% total-amino-acid identity with human FOXN5, 53.8% total-amino-acid identity with mouse Foxn6 (277 aa), and 52.4% total-amino-acid identity with rat Foxn6 (277 aa). Codon 167-248 of human FOXN6 was the Forkhead domain. FN56 domain (codon 1-69 of FOXN6) was identified as a novel domain conserved among FOXN6 and FOXN5 orthologs. Mammalian FOXN6 orthologs were found consisting of FN56 and FOX domains. Phylogenetic analyses revealed that FOXN family proteins are classified into three subfamilies: i) FOXN6 and FOXN5 orthologs; ii) FOXN1 and FOXN4 orthologs; iii) FOXN2 and FOXN3 orthologs. This is the first report on human FOXN6, mouse Foxn6, and rat Foxn6 genes.

No association between variation of the FOXP3 gene and common type 1 diabetes in the Sardinian population.

Mutations of the forkhead/winged helix transcription factor FOXP3 gene on chromosome Xp11.23 cause a rare recessive monogenic disorder called IPEX (immune dysregulation, polyendocrinopathy, including type 1 diabetes, enteropathy, and X-linked syndrome). FOXP3 is necessary for the differentiation of a key immune suppressive subset of T-cells, the CD4+CD25+ regulatory T-cells. Previously, we reported a significant male-female bias in the common, multifactorial form of type 1 diabetes in Sardinia and evidence of linkage of chromosome Xp11 to the disease. These findings indicate that FOXP3 is a prime functional and positional candidate locus for the common form of type 1 diabetes. In the present study, we initially scanned 82 kb of the FOXP3 region for common polymorphisms, including sequencing all of the coding and functionally relevant portions of the gene in 64 Sardinian individuals. Then the most informative polymorphisms in 418 type 1 diabetic families and in 268 male case and 326 male control subjects were sequentially genotyped and tested for disease association. There is no evidence that variants in the FOXP3 regions analyzed are associated with type 1 diabetes and account for the male-female bias observed in Sardinia. Our data indicate that allelic variation in or near the coding regions of the FOXP3 gene does not have a major role in the inherited susceptibility to the common form of type 1 diabetes.

Molecular genetics of autism spectrum disorder.

We are on the brink of exciting discoveries into the molecular genetic underpinnings of autism spectrum disorder. Overwhelming evidence of genetic involvement coupled with increased societal attention to the disorder has drawn in more researchers and more research funding. Autism is a strongly genetic yet strikingly complex disorder, in which evidence from different cases supports chromosomal disorders, rare single gene mutations, and multiplicative effects of common gene variants. With more and more interesting yet sometimes divergent findings emerging every year, it is tempting to view these initial molecular studies as so much noise, but the data have also started to coalesce in certain areas. In particular, recent studies in families with autism spectrum disorder have identified uncommon occurrences of a novel genetic syndrome caused by disruptions of the NLGN4 gene on chromosome Xp22. Previous work had identified another uncommon syndrome that is caused by maternal duplications of the chromosome 15q11-13 region. We highlight other converging findings, point toward those areas most likely to yield results, and emphasize the contributions of multiple approaches to identifying the genes of interest.