A new dimension for the human genome project: towards comprehensive expression maps.

The current Human Genome Project is largely devoted to structural characterisation of our genome. We now need international co-ordination of a second phase of genome analysis, the systematic construction of expression maps using both basic and high-resolution expression assays. Databases recording different types of expression pattern for a variety of human cell types need to be established and co-ordinated. There is a compelling need for a database of gene expression in early human development, but the scarcity of human material for study requires optimisation of research strategies and co-ordination of expression studies in early human and mouse development.

A de novo pathological point mutation at the 21-hydroxylase locus: implications for gene conversion in the human genome.

More than two hundred characterized 21-hydroxylase deficiency alleles appear to result exclusively from sequence exchanges involving the 21-hydroxylase gene (CYP21B) and a closely related pseudogene (CYP21A). Gene conversion-like events have also been reported in many other human gene clusters, but in the absence of a de novo mutation, the alternative explanation of a multiple recombination is possible. We now report a de novo pathological mutation at the 21-hydroxylase locus. DNA sequence analysis suggests that the mutation arose by a microconversion event involving exchange of up to 390 nucleotides between maternal CYP21A and CYP21B genes. This putative de novo gene conversion event appears to be the first characterized in humans.

Mutations in the PAX3 gene causing Waardenburg syndrome type 1 and type 2.

Waardenburg syndrome (WS) is a combination of deafness and pigmentary disturbances, normally inherited as an autosomal dominant trait. The pathology involves neural crest derivatives, but WS is heterogeneous clinically and genetically. Some type I WS families show linkage with markers on distal 2q and in three cases the disease has been attributed to mutations in the PAX3 gene. PAX3 encodes a paired domain, a highly conserved octapeptide and probably also a paired-type homeodomain. Here we describe a further three PAX3 mutations which cause WS; one alters the octapeptide motif plus the presumed homeodomain; a second alters all three elements and the third alters the paired box alone. The latter occurs in a family with probable type 2 WS, a clinical variant usually considered not to be allelic with type 1 WS.

A gene for autosomal dominant sacral agenesis maps to the holoprosencephaly region at 7q36.

Sacral agenesis is a rare disorder of uncertain incidence that has been reported in diverse populations. Although usually sporadic and most commonly associated with maternal diabetes, there is a hereditary form which may occur in isolation or with a presacral mass (anterior meningocele and/or presacral teratoma) and anorectal abnormalities, which constitute the Currarino triad (MIM 176450). The radiological hallmark of hereditary sacral agenesis is a hemi-sacrum (sickle-shaped sacrum) with intact first sacral vertebra. Bowel obstruction is the usual neonatal presentation, but, unlike other neural tube defects, adult presentation is not uncommon. The major pathology is confined to the pelvic cavity and may present as a space-occupying lesion or meningitis due to ascending infection. All recurrences in families have been compatible with autosomal dominant inheritance except for those associated with the isomerism gene at Xq24-q27.1 (ref. 3). Several associated cytogenetic defects have been reported, including 7q deletions. Previous studies failed to detect linkage to HLA markers, but we now present evidence for a location on 7q36. The same region also contains a gene for holoprosencephaly, an early malformation of the extreme rostral end of the neural tube.

Inversin, a novel gene in the vertebrate left-right axis pathway, is partially deleted in the inv mouse.

Visceral left-right asymmetry occurs in all vertebrates, but the inversion of embryo turning (inv) mouse, which resulted following a random transgene insertion, is the only model in which these asymmetries are consistently reversed. We report positional cloning of the gene underlying this recessive phenotype. Although transgene insertion was accompanied by neighbouring deletion and duplication events, our YAC phenotype rescue studies indicate that the mutant phenotype results from the deletion. After extensively characterizing the 47-kb deleted region and flanking sequences from the wild-type mouse genome, we found evidence for only one gene sequence in the deleted region. We determined the full-length 5.5-kb cDNA sequence and identified 16 exons, of which exons 3-11 were eliminated by the deletion, causing a frameshift. The novel gene specifies a 1062-aa product with tandem ankyrin-like repeat sequences. Characterization of complementing and non-complementing YAC transgenic families revealed that correction of the inv mutant phenotype was concordant with integration and intact expression of this novel gene, which we have named inversin (Invs).

Holt-Oram syndrome is caused by mutations in TBX5, a member of the Brachyury (T) gene family.

Holt-Oram syndrome is a developmental disorder affecting the heart and upper limb, the gene for which was mapped to chromosome 12 two years ago. We have now identified a gene for this disorder (HOS1). The gene (TBX5) is a member of the Brachyury (T) family corresponding to the mouse Tbx5 gene. We have identified six mutations, three in HOS families and three in sporadic HOS cases. Each of the mutations introduces a premature stop codon in the TBX5 gene product. Tissue in situ hybridization studies on human embryos from days 26 to 52 of gestation reveal expression of TBX5 in heart and limb, consistent with a role in human embryonic development.

Mutations in ATP2A2, encoding a Ca2+ pump, cause Darier disease.

Darier disease (DD) is an autosomal-dominant skin disorder characterized by loss of adhesion between epidermal cells (acantholysis) and abnormal keratinization. Recently we constructed a 2.4-Mb, P1-derived artificial chromosome contig spanning the DD candidate region on chromosome 12q23-24.1. After screening several genes that mapped to this region, we identified mutations in the ATP2A2 gene, which encodes the sarco/endoplasmic reticulum Ca2(+)-ATPase type 2 isoform (SERCA2) and is highly expressed in keratinocytes. Thirteen mutations were identified, including frameshift deletions, in-frame deletions or insertions, splice-site mutations and non-conservative missense mutations in functional domains. Our results demonstrate that mutations in ATP2A2 cause DD and disclose a role for this pump in a Ca(2+)-signalling pathway regulating cell-to-cell adhesion and differentiation of the epidermis.

A gene related to Caenorhabditis elegans spermatogenesis factor fer-1 is mutated in limb-girdle muscular dystrophy type 2B.

The limb-girdle muscular dystrophies are a genetically heterogeneous group of inherited progressive muscle disorders that affect mainly the proximal musculature, with evidence for at least three autosomal dominant and eight autosomal recessive loci. The latter mostly involve mutations in genes encoding components of the dystrophin-associated complex; another form is caused by mutations in the gene for the muscle-specific protease calpain 3. Using a positional cloning approach, we have identified the gene for a form of limb-girdle muscular dystrophy that we previously mapped to chromosome 2p13 (LGMD2B). This gene shows no homology to any known mammalian gene, but its predicted product is related to the C. elegans spermatogenesis factor fer-1. We have identified two homozygous frameshift mutations in this gene, resulting in muscular dystrophy of either proximal or distal onset in nine families. The proposed name 'dysferlin' combines the role of the gene in producing muscular dystrophy with its C. elegans homology.

A homeobox gene, HLXB9, is the major locus for dominantly inherited sacral agenesis.

Partial absence of the sacrum is a rare congenital defect which also occurs as an autosomal dominant trait; association with anterior meningocoele, presacral teratoma and anorectal abnormalities constitutes the Currarino triad (MIM 176450). Malformation at the caudal end of the developing notochord at approximately Carnegie stage 7 (16 post-ovulatory days), which results in aberrant secondary neurulation, can explain the observed pattern of anomalies. We previously reported linkage to 7q36 markers in two dominantly inherited sacral agenesis families. We now present data refining the initial subchromosomal localization in several additional hereditary sacral agenesis (HSA) families. We excluded several candidate genes before identifying patient-specific mutations in a homeobox gene, HLXB9, which was previously reported to map to 1q41-q42.1 and to be expressed in lymphoid and pancreatic tissues.

Association of selected inflammatory biomarkers with cough reflex sensitivity in asthmatic children.

Bronchial asthma is the most common chronic respiratory disease of childhood. Cough is one of its defining symptoms. This study investigated the associations between selected inflammatory biomarkers and cough reflex sensitivity after capsaicin inhalation in children with mild and moderate well-controlled type 2 endotype asthma compared with non-asthmatic probands. Sensitivity to the cough reflex was measured by recording the cough response after capsaicin inhalation. The sandwich ELISA method was used to measure serum concentrations of the investigated potential inflammatory biomarkers (interleukin 13, interleukin 1beta, eosinophil-derived neurotoxin). The acquired data were statistically evaluated according to descriptive analyses for summarization and comparison between cough reflex sensitivity parameters and individual biomarker values in the observed and control groups modeled by a simple linear regression model. Statistical significance was defined as p<0.05. We showed a statistically significant association (p-value 0.03) between cough reflex sensitivity - C2 value (capsaicin concentration required for two cough responses) and interleukin 1beta serum concentrations in the asthma group compared with the control group of non-asthmatic children. Our results support the possibility of interleukin 1beta as a potential additive inflammatory biomarker used in clinical practice in children with asthma because of its correlation with the activity of the afferent nerve endings in the airways.

PAX genes.

PAX genes are developmental control genes that encode transcription factors containing a DNA-binding paired domain. Mutations in three of the nine mouse genes (Pax1, Pax3 and Pax6) and two of the nine human genes (PAX3 and PAX6) are known to cause developmental defects. These defects are caused by loss-of-function alleles; pathogenesis occurs as a result of a half dosage of the PAX gene product in particular cells. Gain-of-function mutations have been implicated in cancer.

A novel human Wnt gene, WNT10B, maps to 12q13 and is expressed in human breast carcinomas.

Several members of the Wnt gene family have been shown to cause mammary tumors in mouse. Using degenerate primer polymerase chain reaction (PCR) on human genomic DNA, and specific PCR of cDNA libraries, we have isolated a WNT gene which has not previously been described in human. The gene is the human homologue of mouse Wnt10b, recently shown to be one of the oncogenes cooperating with FGF3 in the development of mouse mammary tumour virus (MMTV) induced mouse mammary carcinomas. The human WNT10B sequence was 88% and 95% identical to the murine gene at nucleotide and amino acid levels, respectively. YAC FISH mapping localises the gene to 12q13, a chromosomal region frequently rearranged in human tumours and also containing the WNT1 gene. In normal and benign proliferations of human breast tissue, WNT10B expression was not detected by ribonuclease protection assays but was found at low levels in RT-PCR experiments. In contrast, using both methods, WNT10B expression was found to be elevated in 3 of 50 primary breast carcinomas. Southern blot analysis of the carcinoma expressing the highest levels of WNT10B showed no amplification or rearrangement of the gene. The WNT10B gene was also expressed in some cancer and non cancerous breast cell lines. These findings suggest that the WNT10B gene may be involved in human breast cancer, and show that there is differential expression of the WNT10B gene in benign and malignant disease.

Expression of steroidogenic factor 1 and Wilms' tumour 1 during early human gonadal development and sex determination.

The transcription factors SF-1 and WT1 play pivotal roles in mammalian gonadal development and sexual differentiation. In human embryos, both SF-1 and WT1 are expressed when the indifferent gonadal ridge first forms at 32 days post-ovulation. As the sex cords develop - providing morphological evidence of testis differentiation - SF-1 localises predominantly to developing Sertoli cells in the sex cords, whereas WT1 retains a broader pattern of expression. Later, SF-1 localises predominantly to steroidogenic Leydig cells, and WT1 localises to the sex cords. In the ovary, SF-1 and WT1 transcripts persist in the gonadal ridge from the earliest developmental stages throughout the critical period of sex determination. These studies, which delineate for the first time the sequential expression profiles of SF-1 and WT1 during human gonadal development, provide a framework for understanding human sex reversal phenotypes associated with their mutations.

SRY, SOX9, and DAX1 expression patterns during human sex determination and gonadal development.

SRY, SOX9, and DAX1 are key genes in human sex determination, by virtue of their associated male-to-female sex reversal phenotypes when mutated (SRY, SOX9) or over-expressed (DAX1). During human sex determination, SRY is expressed in 46,XY gonads coincident with sex cord formation, but also persists as nuclear protein within Sertoli cells at 18 weeks gestation. High-level SOX9 expression in the sex cords of the testis parallels that seen during mouse development, however in humans, SOX9 transcripts also are detected in the developing ovary. Low-level DAX1 expression predates peak SRY expression by at least 10 days, and persists in Sertoli cells throughout the entire sex determination period. In Dosage Sensitive Sex reversal, the anti-testis properties of DAX1 over-expression could act prior to the peak effects of SRY and continue during the period of SOX9 expression. These findings highlight expression differences for the SRY, SOX9, and DAX1 genes during sex determination in humans and mice. These results provide a direct framework for future investigation into the mechanisms underlying normal and abnormal human sex determination.

Molecular genetics of congenital adrenal hyperplasia.

More than 95% of cases of congenital adrenal hyperplasia are attributable to steroid 21-hydroxylase (21-OH) deficiency. In normal individuals, there are usually two 21-OH genes on each chromosome 6, a functional 21-OH gene-CYP21B-and a closely related 21-OH pseudogene-CYP21A-which is defective in expression. Recent advances have shown that the pathologic mutations that contribute to 21-OH deficiency arise as a consequence of unequal crossover and gene conversion-like mechanisms that involve sequence interaction between the normally functional 21-OH gene and its pseudogene.

Autosomal dominant sacral agenesis: Currarino syndrome.

Autosomal dominant sacral agenesis is characterised by a partial agenesis of the sacrum typically involving sacral vertebrae S2-S5 only. Associated features include anorectal malformation, a presacral mass, and urogenital malformation. Together, these features have been defined as the Currarino syndrome. Recently, HLXB9 has been identified as the major causative gene in Currarino syndrome allowing identification of asymptomatic heterozygotes. In this review, we have performed an analysis of medical publications, and our own additional cases, to identify the range of malformations and complications that occur. We have also estimated risks of malformation in heterozygotes by using Weinburg's proband method on families personally known to us in order to provide accurate genetic counselling information.

Isolation, characterisation and embryonic expression of WNT11, a gene which maps to 11q13.5 and has possible roles in the development of skeleton, kidney and lung.

The Wnt gene family encodes a set of signalling molecules, thought to play an important role in key processes of embryonic development. In vertebrates as a whole 20 different Wnt genes have been identified to date, however, a complement of only 16 have been identified in man and for some of these the complete coding sequences are unavailable. We have recently isolated the full-length cDNA sequence of a new human WNT gene, WNT11, investigated its genomic organisation and performed detailed expression studies in early human embryos. These have shown that the expression of human WNT11 is restricted to the perichondrium of the developing skeleton, lung mesenchyme, the tips of the ureteric buds and other areas of the urogenital system and the cortex of the adrenal gland. This, for the first time, provides information for the embryonic expression of human WNT11. We have mapped WNT11 to 11q13.5 and this together with its expression in the perichondrium of the developing skeleton, makes it a plausible candidate gene for HBM, which has been previously linked to markers from this region.

Isolation of a full-length human WNT7A gene implicated in limb development and cell transformation, and mapping to chromosome 3p25.

The Wnt gene family has a role in development as well as tumourigenesis. One mouse member, Wnt7a, is vital for limb development in vivo and also possesses transforming ability in vitro. This study reports the isolation of a full length of human homologue of mouse Wnt7a gene by library screening. Yeast artificial chromosome-fluorescence in situ hybridisation (YAC-FISH) mapped the WNT7A gene to chromosome 3p25. Human WNT7A had an ORF encoding a deduced protein of 349 aa that exhibited 97% and 92% identity to mouse Wnt7a at the aa and nucleic acid levels, respectively. It possessed the 22 conserved cysteine residues and 3 more at the amino terminus, and a putative poly A tail. This is the fifth human WNT gene in which a complete cDNA sequence had been determined.

Presymptomatic DNA and MRI diagnosis of neurofibromatosis 2 with mild clinical course in an extended pedigree.

Neurofibromatosis 2 (NF2), a dominantly inherited disorder, typically manifests as bilateral vestibular schwannomas and predisposes to other nervous system tumors. In this study, we present a large pedigree with a benign course of NF2 (mild Gardner type) characterized by slowly growing vestibular schwannomas but few other manifestations. The family was thoroughly investigated with neurologic, ophthalmologic, and neuro-otologic methods including gadolinium-enhanced MRI of the head and spine and DNA linkage analysis. In the clinical analysis of 22 family members, MRI was superior to neuro-otologic methods in the detection of asymptomatic tumors. Based on the DNA linkage analyses we identified the NF2 mutation carriers with a high degree of certainty. These DNA markers (CRYB2, NEFH, D22S268, and D22S280) can also be used for presymptomatic diagnosis in other NF2 families. Early detection of NF2 gene mutation carriers has become possible using linkage analysis in familial NF2. MRI screening of carriers will reveal presymptomatic vestibular schwannomas (and other CNS tumors), making early intervention possible, but an efficient treatment strategy to prevent deafness has not yet been established.