Isolation of a diverged homeobox gene, MOX1, from the BRCA1 region on 17q21 by solution hybrid capture

The role of MEOX1 in non-neoplastic and neoplastic diseases

Targeted gene therapy has shown durable efficacy in non-neoplastic and neoplastic patients. Therefore, finding a suitable target has become a key area of research. Mesenchyme homeobox 1 (MEOX1) is a transcriptional factor that plays a significant role in regulation of somite development. Evidence indicates that abnormalities in MEOX1 expression and function are associated with a variety of pathologies, including non-neoplastic and neoplastic diseases. MEOX1 expression is upregulated during progression of most diseases and plays a critical role in maintenance of the cellular phenotypes such as cell differentiation, cell cycle arrest and senescence, migration, and proliferation. Therefore, MEOX1 may become an important molecular target and therapeutic target. This review will discuss the current state of knowledge on the role of MEOX1 in different diseases.

Genomic, Clinical, and Behavioral Characterization of 15q11.2 BP1-BP2 Deletion (Burnside-Butler) Syndrome in Five Families

The 15q11.2 BP1-BP2 deletion (Burnside-Butler) syndrome is emerging as the most common cytogenetic finding in patients with neurodevelopmental or autism spectrum disorders (ASD) presenting for microarray genetic testing. Clinical findings in Burnside-Butler syndrome include developmental and motor delays, congenital abnormalities, learning and behavioral problems, and abnormal brain findings. To better define symptom presentation, we performed comprehensive cognitive and behavioral testing, collected medical and family histories, and conducted clinical genetic evaluations. The 15q11.2 BP1-BP2 region includes the TUBGCP5, CYFIP1, NIPA1, and NIPA2 genes. To determine if additional genomic variation outside of the 15q11.2 region influences expression of symptoms in Burnside-Butler syndrome, whole-exome sequencing was performed on the parents and affected children for the first time in five families with at least one parent and child with the 15q1l.2 BP1-BP2 deletion. In total, there were 453 genes with possibly damaging variants identified across all of the affected children. Of these, 99 genes had exclusively de novo variants and 107 had variants inherited exclusively from the parent without the deletion. There were three genes (APBB1, GOLGA2, and MEOX1) with de novo variants that encode proteins evidenced to interact with CYFIP1. In addition, one other gene of interest (FAT3) had variants inherited from the parent without the deletion and encoded a protein interacting with CYFIP1. The affected individuals commonly displayed a neurodevelopmental phenotype including ASD, speech delay, abnormal reflexes, and coordination issues along with craniofacial findings and orthopedic-related connective tissue problems. Of the 453 genes with variants, 35 were associated with ASD. On average, each affected child had variants in 6 distinct ASD-associated genes (x¯ = 6.33, sd = 3.01). In addition, 32 genes with variants were included on clinical testing panels from Clinical Laboratory Improvement Amendments (CLIA) approved and accredited commercial laboratories reflecting other observed phenotypes. Notably, the dataset analyzed in this study was small and reported results will require validation in larger samples as well as functional follow-up. Regardless, we anticipate that results from our study will inform future research into the genetic factors influencing diverse symptoms in patients with Burnside-Butler syndrome, an emerging disorder with a neurodevelopmental behavioral phenotype.

Recent advances in liquid hydrosilane-mediated catalytic N-formylation of amines with CO2

Carbon dioxide is an ideal raw material for the synthesis of complex organic compounds because of its rich, non-toxic, and good physical properties. It is of great significance to transform CO₂ into valuable fine chemicals and develop a green sustainable cycle of carbon surplus. Based on hydrosilane as a reducing agent, this work summarizes the recent applications of reductive amidation of CO₂ using different catalysts such as organocatalysts, ionic liquids (ILs), salts, transition metal complexes, and solvents. The main factors affecting the reductive amidation of CO₂ and the possible reaction mechanism are discussed. Moreover, the future orientation and catalytic systems of the formylation of amines with CO₂ and hydrosilane are prospected.

This review depicts different types of catalyst systems developed for upgrading of amines and carbon dioxide into N-formylated products in the presence of hydrosilane, with attention on reaction mechanism and process optimization.

Regulation and function of homeodomain proteins in the embryonic and adult vascular systems

During embryonic development, the cardiovascular system first forms and then gives rise to the lymphatic vascular system. Homeobox genes are essential for both the development of the blood and lymphatic vascular systems, as well as for their maintenance in the adult. These genes all encode proteins that are transcription factors that contain a well conserved DNA binding motif, the homeodomain. It is through the homeodomain that these transcription factors bind to the promoters of target genes and regulate their expression. Although many homeodomain proteins have been found to be expressed within the vascular systems, little is known about their downstream target genes. This review highlights recent advances made in the identification of novel genes downstream of the homeodomain proteins that are necessary for regulating vascular cellular processes such as proliferation, migration, and endothelial tube formation. Factors known to regulate the functions of vascular cells via modulating the expression of homeobox genes will be discussed. We will also review current methods used to identify and characterize downstream target genes of homeodomain proteins.

The regulation of ER-α transcription by pRb2/p130 in breast cancer

Breast carcinoma is the most common form of neoplasia in women of the Western world, and the mortality from this disease in women is second only to that of lung cancer, with a means incidence of 10%. Although, several studies have indicated that the development of this fairly heterogeneous disease depends on a great many environmental, socio-economic, hormonal and genetic factors, the pathogenesis of breast cancer remains poorly understood. ER-alpha (estrogen-receptor alpha) and its ligand (17beta-estradiol) play a crucial role in normal breast development and have also been linked to mammary carcinogenesis and clinical outcome in breast cancer patients. The estrogen signaling regulates the growth of some breast tumors, and antiestrogen therapies can effectively block this growth signaling resulting in tumor suppression. However, most tumors eventually develop antiestrogen resistance, and antiestrogen are mostly ineffective in patience with advanced disease. Although several studies have been proposed that epigenetic events could be involved in ER-alpha silencing the mechanisms regulating ER-alpha transcription are poorly understood. Our studies suggested that pRb2/p130-complexes bind to the ER-alpha promoter and could be involved in the transcriptional regulation of the ER-alpha gene by altering chromatin structure and DNA methylation pattern.

Exploring alternative transcript structure in the human genome using blocks and InterPro

Understanding how alternative splicing affects gene function is an important challenge facing modern-day molecular biology. Using homology-based, protein sequence analysis methods, it should be possible to investigate how transcript diversity impacts protein function. To test this, high-quality exon-intron structures were deduced for over 8000 human genes, including over 1300 (17 percent) that produce multiple transcript variants. A data mining technique (DiffMotif) was developed to identify genes in which transcript variation coincides with changes in conserved motifs between variants. Applying this method, we found that 30 percent of the multi-variant genes in our test set exhibited a differential profile of conserved InterPro and/or BLOCKS motifs across different mRNA variants. To investigate these, a visualization tool (ProtAnnot) that displays amino acid motifs in the context of genomic sequence was developed. Using this tool, genes revealed by the DiffMotif method were analyzed, and when possible, hypotheses regarding the potential role of alternative transcript structure in modulating gene function were developed. Examples of these, including: MEOX1, a homeobox-containing protein; AIRE, involved in auto-immune disease; PLAT, tissue type plasminogen activator; and CD79b, a component of the B-cell receptor complex, are presented. These results demonstrate that amino acid motif databases like BLOCKS and InterPro are useful tools for investigating how alternative transcript structure affects gene function.

WWOX, the common chromosomal fragile site, FRA16D, cancer gene

Gross chromosomal rearrangements and aneuploidy are among the most common somatic genomic abnormalities that occur during cancer initiation and progression, in particular in human solid tumor carcinogenesis. The loss of large chromosomal regions as consequence of gross rearrangements (e.g. deletions, monosomies, unbalanced translocations and mitotic recombination) have been traditionally associated with the existence of tumor suppressor genes within the areas affected by the loss of genetic material. The long arm of chromosome 16 was identified as being frequently associated with structural abnormalities in multiple neoplasias, that led us to focus attention on the detailed genetic dissection of this region resulting in the cloning of the putative tumor suppressor gene, WWOX (WW domain containing Oxidoreductase). Interestingly, the WWOX gene resides in the very same region as that of the common chromosomal fragile site 16D (FRA16D). The WWOX gene encodes a protein that contains two WW domains, involved in protein-protein interactions, and a short chain dehydrogenase (SDR) domain, possibly involved in sex-steroid metabolism. We have identified the WWOX WW domain ligand as the PPXY motif confirming the biochemical activity of this domain. WWOX normally resides in the Golgi and we will demonstrate that Golgi localization requires an intact SDR. Inactivation of the WWOX gene during tumorigenesis can occur by homozygous deletions and possibly mutation, however, aberrantly spliced forms of WWOX mRNA have been observed even when one allele is still intact. The aberrantly spliced mRNAs have deletions of the exons that encode the SDR and these WWOX protein isoforms display abnormal intracellular localization to the nucleus possibly functioning as dominant negative inhibitors of full length WWOX. Thus, generation of aberrant transcripts of WWOX may represent a novel mechanism to functionally inactivate WWOX without genomic alteration of the remaining allele. In this article we will review the cloning and identification of WWOX as the target of FRA16D. In addition, we will discuss the possible biochemical functions of WWOX and present evidence that ectopic WWOX expression inhibits tumor growth.

Refined mapping of Naegeli-Franceschetti- Jadassohn syndrome to a 6 cM interval on chromosome 17q11.2-q21 and investigation of candidate genes

Naegeli-Franceschetti-Jadassohn syndrome and dermatopathia pigmentosa reticularis are autosomal dominant ectodermal dysplasias characterized by the absence of dermatoglyphics, reticulate hyper pigmentation of the skin, hypohidrosis, and heat intolerance. Palmoplantar keratoderma, nail dystrophy, and enamel defects are common in Naegeli-Franceschetti-Jadassohn syndrome, whereas diffuse alopecia is only seen in dermatopathia pigmentosa reticularis. We studied a large Swiss family with Naegeli-Franceschetti-Jadassohn syndrome originally described by Naegeli in 1927 and assessed linkage to chromosome 17q, which was proposed to harbor the Naegeli-Franceschetti-Jadassohn syndrome gene. Our results considerably narrow the Naegeli-Franceschetti-Jadassohn syndrome gene region from 27 cM to 6 cM flanked by D17S933 and D17S934 with a maximum multipoint LOD score of 2.7 at marker locus D17S800. In addition, we studied a small family with dermatopathia pigmentosa reticularis, and our linkage data suggest that dermatopathia pigmentosa reticularis may map to the same chromosomal region. The Naegeli-Franceschetti-Jadassohn syndrome critical interval spans approximately 5.4 Mb and contains a minimum of 45 distinct genes. We scrutinized 13 new prime candidates in addition to five genes previously examined, established the genomic organization of 10 of these genes, and excluded all of them by mutation analysis. Moreover, we identified a cDNA (KRT24) encoding a new keratin protein that bears high similarity to the type I keratins and displays a unique expression profile. No pathogenic mutations were identified in this novel gene either, however. In summary, our results substantially refine the Naegeli-Franceschetti-Jadassohn syndrome region and will aid in identifying a gene that is critical for ontogenesis of multiple ectodermal tissues.

The single amphioxus Mox gene: insights into the functional evolution of Mox genes, somites, and the asymmetry of amphioxus somitogenesis

Mox genes are members of the "extended" Hox-cluster group of Antennapedia-like homeobox genes. Homologues have been cloned from both invertebrate and vertebrate species, and are expressed in mesodermal tissues. In vertebrates, Mox1 and Mox2 are distinctly expressed during the formation of somites and differentiation of their derivatives. Somites are a distinguishing feature uniquely shared by cephalochordates and vertebrates. Here, we report the cloning and expression of the single amphioxus Mox gene. AmphiMox is expressed in the presomitic mesoderm (PSM) during early amphioxus somitogenesis and in nascent somites from the tail bud during the late phase. Once a somite is completely formed, AmphiMox is rapidly downregulated. We discuss the presence and extent of the PSM in both phases of amphioxus somitogenesis. We also propose a scenario for the functional evolution of Mox genes within chordates, in which Mox was co-opted for somite formation before the cephalochordate-vertebrate split. Novel expression sites found in vertebrates after somite formation postdated Mox duplication in the vertebrate stem lineage, and may be linked to the increase in complexity of vertebrate somites and their derivatives, e.g., the vertebrae. Furthermore, AmphiMox expression adds new data into a long-standing debate on the extent of the asymmetry of amphioxus somitogenesis.

Expression of homeobox genes in cervical cancer

OBJECTIVE

Members of the homeobox (HB) gene superfamily encode transcription factors crucial for development and may be associated with tumorigenesis. In this study, we aimed to develop a procedure to survey the expression of the dispersed-type HB genes in cervical cancer cells.

METHODS

Nineteen sets of degenerate primers were designed based on conserved homeodomains of known dispersed-type HB genes. A cDNA library derived from HeLa, a cervical cancer cell line, was used. Two successive rounds of PCR were performed using a combination of the HB degenerate primers and a primer recognizing the flanking sequence of the vector used in the cDNA library construction.

RESULTS

On cloning and sequence analysis of the PCR fragments generated, 10 known and 3 putative novel HB genes were detected in HeLa. RT-PCR expression analysis further showed that HOXD9 and ATBF1 were differentially expressed in cancer cells and not in normal cervix.

CONCLUSIONS

Our data demonstrate the feasibility of using degenerate primers in PCR experiments in a collective analysis of complex gene families. Our data indicate that HOXD9 and ATBF1 are expressed in cervical cancer, but not in normal cervix.

A tissue specific IL-1 receptor antagonist homolog from the IL-1 cluster lacks IL-1, IL-1ra, IL-18 and IL-18 antagonist activities

Interleukin (IL)-1-like protein 1 (IL-1L1) is a 155-amino acid protein that shares 27% identity with IL-1beta and 47% with IL-1 receptor antagonist (IL-1ra). A 2.7-kb IL-1L1 mRNA was cloned from human placenta and is detectable in the trophoblastic cell line JEG-3, in macrophages and in endotoxin-stimulated monocytes. Expression of IL-1L1 is much less abundant and less widespread than IL-1ra. We have determined the human and mouse IL-1L1 cDNA sequences and the complete sequence of the human gene, IL1L1. IL1L1 consists of four coding exons, has two alternative non-coding first exons, lies between IL1B and IL1RN, is orientated in the same direction as IL1RN and is separated from it by approximately 53 kb. The predicted IL-1L1 protein lacks both signal sequence and glycosylation signals. A 17-kDa protein was recovered by immunoprecipitation with IL-1L1-specific antibodies from JEG-3. IL-1L1 did not stimulate IL-6 production from primary human fibroblasts or human umbilical vein endothelial cells nor did it block the IL-1alpha or IL-1beta-dependent activation of IL-6 expression. We conclude, contrary to a recent suggestion made by others, that IL-1L1 is not a functional IL-1ra. IL-1L1 also had no detectable agonistic or antagonistic effect on IFN-gamma production in response to IL-18 in KG-1 cells.

The gene for Naegeli-Franceschetti-Jadassohn syndrome maps to 17q21

Naegeli-Franceschetti-Jadassohn syndrome is a rare autosomal dominant form of ectodermal dysplasia affecting sweat glands, nails, teeth, and skin. We have studied a multigeneration family of Anglo-Saxon British descent using microsatellite markers to screen candidate loci, including the epidermal differentiation complex on 1q, the keratin gene clusters on chromosomes 12q and 17q and the desmosomal cadherin gene cluster on chromosome 18q. Significant genetic linkage to chromosome 17q was observed using marker D17S 1787, with a maximum two-point LOD score of 4.166 at a recombination fraction of theta = 0. Recombination events in the family place the gene in a 26.97 cM interval between markers D17S798 and D17S957, a region known to contain the type I keratin gene cluster and other genes expressed in epithelia. Keratins K15, K19, and K20, plakoglobin, and MEOX1 were excluded as candidates by direct sequencing of genomic polymerase chain reaction products.

The rate of the founder Jewish mutations in BRCA1 and BRCA2 in prostate cancer patients in Israel

Inherited predisposition occurs in 5-10% of all prostate cancer (CaP) patients, but the genes involved in conferring genetic susceptibility remain largely unknown. Several lines of evidence indicate that germline mutations in BRCA1 and BRCA2 might be associated with an increased risk for CaP. Three mutations in these two genes (185delAG and 5382InsC (BRCA1) and 6174delT (BRCA2) occur in about 2.5% of the general Ashkenazi population, and the 185delAG BRCA1 mutation, in up to 1% of non-Ashkenazi Jews. In order to assess the contribution of these germline mutations to prostate cancer in Jewish Israeli patients, we tested 174 unselected prostate cancer patients (95 of Ashkenazi origin) for these mutations by PCR amplification and modified restriction enzyme digests. Patient's age range was 45-81 years (median 66), and in 24 (14.4%) the disease was diagnosed prior to 55 years of age. Nineteen (11%) and 12 (6.9%) patients had a first or second degree relative with CaP or breast cancer, respectively. Overall, five mutation carriers were detected: 2/152 (1.3%) 185delAG, 2/104 (2%) 5382InsC, and 1/158 (0.6%) 6174delT. In all carriers, the disease was diagnosed after the age of 55, and only one of them had a family history of breast and CaP. In addition, no allelic losses at the BRCA1 locus were demonstrated in 17 patients with a family history of CaP, using seven microsatellite markers. We conclude that the rate of the predominant Jewish BRCA1 and BRCA2 mutations in CaP patients does not significantly differ from that of the general population, and that mutational inactivation of the BRCA1 is rare in familial CaP. Thus, germline BRCA1 and BRCA2 mutations probably contribute little to CaP occurrence, to inherited predisposition, and to early onset disease in Jewish individuals.

Identification of the familial cylindromatosis tumour-suppressor gene

Familial cylindromatosis is an autosomal dominant genetic predisposition to multiple tumours of the skin appendages. The susceptibility gene (CYLD) has previously been localized to chromosome 16q and has the genetic attributes of a tumour-suppressor gene (recessive oncogene). Here we have identified CYLD by detecting germline mutations in 21 cylindromatosis families and somatic mutations in 1 sporadic and 5 familial cylindromas. All mutations predict truncation or absence of the encoded protein. CYLD encodes three cytoskeletal-associated-protein-glycine-conserved (CAP-GLY) domains, which are found in proteins that coordinate the attachment of organelles to microtubules. CYLD also has sequence homology to the catalytic domain of ubiquitin carboxy-terminal hydrolases (UCH).

Genomic and expression analyses of alternatively spliced transcripts of the MLL septin-like fusion gene (MSF) that map to a 17q25 region of loss in breast and ovarian tumors

We previously defined a common region of 17q25 loss in breast and ovarian tumors, suggesting localization of at least one putative tumor suppressor gene. Genomic clones from the interval were used to isolate candidate transcripts. One novel transcript had strong homology to a septin family of GTPase genes involved in cytokinesis. This gene was recently identified as a myeloid/lymphoid leukemia (MLL) fusion protein partner in acute myeloid leukemia and was named MSF (MLL septin-like fusion). As this gene may play roles in both leukemogenesis and tumorigenesis, it is essential to understand its structure and normal expression. We cloned two human alternative transcripts and identified a third database variant of MSF. RNA expression studies with a probe common to the three novel sequences showed differential expression of 4.0- and 3.0-kb transcripts in all adult and fetal tissues tested. A probe spanning sequence unique to one MSF variant detected specific expression of the 4.0-kb transcript in all tissues. Another probe unique to a different MSF variant detected a 4.0-kb transcript only in skeletal muscle. Proteins of 422 and 586 amino acids were predicted from the novel alternate transcripts and included both a xylose isomerase 1 domain and a GTPase domain. Nine common exons, three alternatively spliced exons, and six polymorphisms were identified.

Homeobox genes in mammary gland development and neoplasia

Both normal development and neoplastic progression involve cellular transitions from one physiological state to another. Whereas much is being discovered about signal transduction networks involved in regulating these transitions, little progress has been made in identifying the higher order genetic determinants that establish and maintain mammary cell identity and dictate cell type-specific responses to mammotropic signals. Homeobox genes are a large superfamily of genes whose members function in establishing and maintaining cell fate and cell identity throughout embryonic development. Recent genetic and expression analyses strongly suggest that homeobox genes may perform similar functions at specific developmental transition points in the mammary gland. These analyses also suggest that homeobox genes may play a contributory or causal role in breast cancer.

Homeobox genes in cardiovascular development

As summarized earlier, a surprisingly large number of different homeobox genes are expressed in the developing heart. Some are clearly important, as demonstrated by mouse gene ablation studies. For example, knockout of Nkx2-5 or Hoxa-3 function is embryonic lethal due to defects in cardiovascular development. However, gene ablation studies indicate that other homeobox genes that show cardiovascular expression are either not required for heart development or their function is effectively complemented by a redundant gene activity. Given the number of closely related homeobox genes that are expressed in the heart (and the rate at which new genes are being discovered), this is very likely to be the case for at least some homeobox gene activities. At present little is known of the precise mechanism of action of homeobox genes in embryonic development. This statement applies to homeobox genes in general, not just to genes involved in cardiovascular development. There is a popular view that homeobox genes are master regulators that control expression of a large number of downstream genes. In at least some cases, e.g., the eyeless gene of Drosophila (Holder et al., 1995), homeobox genes appear to be capable of activating and maintaining a very complex developmental program. Significantly, the eyeless gene is able to initiate eye development at numerous ectopic locations. Increasing evidence, however, suggests that genes of this type may be rather rare. Certainly there is no evidence to date that any of the homeobox genes expressed in the heart are able to initiate the complete heart development pathway. This is probably best understood in the case of the tinman gene in Drosophila, which, although absolutely required for heart development, is not capable of initiating the cardiac development pathway in ectopic locations (Bodmer, 1993). This conclusion is supported by studies of the vertebrate tinman-related gene Nkx2-5. Gene ablation studies show that Nkx2-5 is essential for correct cardiac development (Lyons et al., 1995) but is not able to initiate the regulatory pathway leading to cardiac development when expressed ectopically (Cleaver et al., 1996; Chen and Fishman, 1996). If most homeodomain proteins are not direct regulators of a differentiation pathway, what is their role during organogenesis? The cardiovascular homeobox gene about which most is known at the mechanistic level is gax (Smith et al., 1997). A number of experiments indicate that the Gax protein is involved in the regulation of cell proliferation and that it interacts with components of the cell cycle regulation machinery. Indeed, over recent years, the idea that at least some homeobox genes play their role in organogenesis through regulation of proliferation has been developed in some detail by Duboule (1995). Further evidence that this mechanism of homeobox activity is important, especially during organogenesis, comes from studies of the Hox11 homeobox gene, which is absolutely required for development of the spleen in mouse (Roberts et al., 1994). Studies indicate that Hox11 is able to interact with at least two different protein phosphatases, PP2A and PP1, which in turn, are involved in cell cycle regulation (Kawabe et al., 1997). It is quite clear that research in future years will need to focus on the precise mode of action of the different homeodomain proteins if we are to understand their role in the development of the cardiovascular system.

Breast cancer susceptibility genes. BRCA1 and BRCA2

Mutations in the BRCA1 and BRCA2 genes lead to an increased susceptibility to breast, ovarian, and other cancers. It is estimated that 3%-8% of all women with breast cancer will be found to carry a mutation in 1 of these genes. Families with multiple affected first-degree relatives and patients with early-onset disease have been found to harbor mutations at a higher frequency. The BRCA1 and BRCA2 genes code for large proteins that bear no resemblance to other known genes. In the cell, they appear to act as tumor suppressor genes and play a role in the maintenance of genome integrity, although the precise function of these genes has yet to be discovered. A large number of distinct mutations have been found in cancer families around the world. The majority of the defined pathologic mutations result in premature truncation of the protein (frameshift and nonsense mutations). These mutations may substantially increase the risk for breast and ovarian cancer, but a precise risk estimate for each different mutation cannot be determined. Depending on the familial context, the risk of breast cancer associated with carrying a mutation has been estimated to range from 50% to 85%. The role of these genes in sporadic cancer remains unknown. Patients and physicians considering BRCA1 and BRCA2 genetic testing are faced with a difficult decision. The diversity of mutations and lack of general population data prevent accurate risk prediction. This is further complicated by the paucity of data on effective prevention strategies for those identified at higher risk. Thus, the nature of clinical testing for BRCA1 and BRCA2 continues to present challenges that reinforce the necessity of personal choice within the context of thorough genetic counseling.

A serine/threonine kinase gene defective in Peutz-Jeghers syndrome

Studies of hereditary cancer syndromes have contributed greatly to our understanding of molecular events involved in tumorigenesis. Here we investigate the molecular background of the Peutz-Jeghers syndrome (PJS), a rare hereditary disease in which there is predisposition to benign and malignant tumours of many organ systems. A locus for this condition was recently assigned to chromosome 19p. We have identified truncating germline mutations in a gene residing on chromosome 19p in multiple individuals affected by PJS. This previously identified but unmapped gene, LKB1, has strong homology to a cytoplasmic Xenopus serine/threonine protein kinase XEEK1, and weaker similarity to many other protein kinases. Peutz-Jeghers syndrome is therefore the first cancer-susceptibility syndrome to be identified that is due to inactivating mutations in a protein kinase.

Novel transcribed sequences within the BWS/WT2 region in 11p15.5: tissue-specific expression correlates with cancer type

Chromosome band 11p15.5 has proven to be an intriguing area of the human genome. Various studies have linked alterations in this region to growth-related disorders such as Beckwith-Wiedemann syndrome and a variety of human cancers. Furthermore, functional assays in G401 Wilms tumor cells and RD rhabdomyosarcoma cells support the existence of a tumor suppressor gene on 11p15.5, sometimes called WT2. In addition, several genes mapping to this region show imprinted expression, suggesting that 11p15.5 contains an imprinted domain. We have employed solution hybrid capture in combination with sequence analysis to identify 16 genes within the approximately 700-kb critical region of 11p15.5 between D11S601 and D11S1318. Two of these genes, NAP1L4 and KCNA9, had been previously reported. Ten novel transcripts were identified with partial cDNA sequences selected by solution hybrid capture. Sequence homology to known ESTs was used to identify the remaining gene transcripts. Interestingly, the tissue-specific mRNA expression of these genes correlates with the tumor types linked to this region. This work can be compiled into a transcript map, important in the elucidation of tumor suppressor activity on chromosome 11p15.5.

Construction of a transcription map around the gene for ataxia telangiectasia: identification of at least four novel genes

We have constructed YAC, PAC, and cosmid contigs in the ataxia-telangiectasia gene region and used the assembled clones to isolate expressed sequences by exon trapping and hybridization selection. In the interval between D11S1819 and D11S2029, exons and cDNAs for potentially 13 different genes were identified. Three of these genes, F37, K28, and 6.82, are large novel genes expressed in a variety of different tissues. K28 shows sequence homology to the Rab GTP binding protein family and gene 6.82 homology to the rabbit vasopressin activated calcium mobilizing receptor, while gene F37 has no homology to any known sequence in the database. Three further clones, exon 6.41 and cDNAs K22 and E74, from the interval between D11S1819 and D11S2029, appear to be expressed endogenous retrovirus sequences. The fourth large novel genes, E14, together with two further possible novel genes, E13 and E3, was identified from exons and cDNAs in the more telomeric 300-kb interval between markers D11S2029 and D11S2179. These are in addition to the genes for mitochondrial acetoacetyl-CoA-acetyltransferase (ACAT) and the ATM gene in the same region. Genes E3, E13, and E14 do not show homology to any known genes. K28, 6.82, ACAT, and ATM all appear to have the same transcriptional orientation toward the telomere.

Identification and analysis of expression of human VACM-1, a cullin gene family member located on chromosome 11q22-23

We have localized the human homolog of the rabbit vasopressin-activated calcium-mobilizing receptor VACM-1 to a region close to the gene for ataxia telangiectasia ATM on chromosome 11q22-23. We have determined the complete amino acid sequence of the human Hs-VACM-1 protein, which is 780 amino acids long. The human and rabbit sequences are highly conserved, differing at only seven amino acids. Northern analysis of the human gene showed expression in a wide range of human tissues. The Hs-VACM-1 gene has homology with the Caenorhabditis elegans gene Ce-cul-5, a member of a family of cullin genes that are involved in cell cycle regulation and that might, when mutated, contribute to tumor progression.

Checklist: vertebrate homeobox genes

Up to now around 170 different homeobox genes have been cloned from vertebrate genomes. A compilation of the various isolates from mouse, chick, frog, fish and man is presented in the form of a concise checklist, including the designations from the original publications. Putative homologs from different species are aligned, and key characteristics of embryonic or adult expression domains, as well as mutant phenotypes are briefly indicated.

Monitoring the efficacy of hybrid selection during positional cloning: the search for BRCA1

Positional cloning often requires isolation of candidate genes from a large, genetically defined region. Hybrid selection (direct cDNA selection, solution hybrid capture) is a rapid, simple procedure that has been used to identify expressed sequence tags (ESTs) from cloned genomic DNA. We used hybrid selection to screen a 600-kb region that includes the BRCA1 gene. From a set of 931 sequenced clones, we obtained 118 nonoverlapping candidate ESTs from ovary and lymphocyte cDNA. We analyzed the results of our hybrid selection experiments with particular attention to the overall completeness, efficiency, and background noise of the experiment. We introduce simple parameters that serve as measures of important aspects of the hybrid selection process in the context of positional cloning.

The expression pattern of Xenopus Mox-2 implies a role in initial mesodermal differentiation

We have isolated a Xenopus homolog of the murine Mox-2 gene. As is the case for the mouse homolog, mesoderm specific expression of Xenopus Mox-2 (X. Mox-2) expression begins during gastrulation. Using whole mount in situ hybridization, we show that X. Mox-2 is expressed in undifferentiated dorsal, lateral and ventral mesoderm in the posterior of neurula/tailbud embryos, with expression more anteriorly detected in the dermatomes. In the tailbud tadpole, X. Mox-2 is expressed in tissues of the tailbud itself that represent a site of continued gastrulation-like processes resulting in mesoderm formation. X. Mox-2 is not expressed in the marginal zone of blastula, nor in the dorsal lip of gastrula, nor midline tissues (i.e. prospective notochord). Treatments that affect mesodermal patterning during embryonic development, including LiCl and ultraviolet light, and injection of mRNAs encoding BMP-4, or dominant negative activin and FGF receptors, produce changes in X. Mox-2 expression consistent with the types of tissues affected by these manipulations. X. Mox-2 expression is induced more in animal caps treated with FGF than those treated with activin. Together with the fact that X. Mox-2 activation in animal caps requires protein synthesis, our data suggest that X. Mox-2 is involved in initial mesodermal differentiation, downstream of molecules affecting mesoderm induction and determination such as Brachyury and goosecoid, and upstream of factors controlling terminal differentiation such as MyoD and myf5. X. Mox-2, therefore, is another useful marker for understanding the formation of mesoderm in amphibian development.

Isolation of the human MOX2 homeobox gene and localization to chromosome 7p22.1-p21.3

We have isolated and characterized cDNA clones encoding a novel human homeobox gene, MOX2, the homologue of the murine mox-2 gene. The MOX2 protein contains all of the characteristic features of Mox-2 proteins of other vertebrate species, namely the homeobox, the polyhistidine stretch, and a number of potential serine/threonine phosphorylation sites. The homeodomain of MOX2 protein is identical to all other vertebrate species reported so far (rodents and amphibians). Outside the homeodomain, Mox-2 proteins share a high degree of identity, except for a few amino acid differences encountered between the human and the rodent polypeptides. A polyhistidine stretch of 12 amino acids in the N terminal region of the protein is also conserved among humans, rodents, and (only partly) amphibians. The chromosomal position of MOX2 was assigned to 7p22.1-p21.3.

Techniques in mammalian genome mapping

Increasing emphasis is being given to genomic cloning using Escherichia coli vectors of intermediate insert capacity, such as bacteriophage P1, P1-derived artificial chromosomes and the F factor based bacterial artificial chromosomes. These vectors are being used in addition to yeast artifical chromosomes (YACs) in recognition of the difficulties encountered with YAC stability and with handling of YAC DNAs (problems that will not easily be overcome). Nonetheless, YACs remain the most practical cloning system for global contig building. Efforts are currently under way to produce YAC contigs that represent the human and mouse genomes, and these will increasingly exploit extensive anchoring to detailed genetic maps. Intermediate capacity clone collections based on YAC contigs will follow, enabling the compilation of mapped gene catalogues. In this way, the era of big gene hunts will draw to a close.

Direct selection of expressed sequences within a 1-Mb region flanking BRCA1 on human chromosome 17q21

Direct selection of genes within the interval of chromosome 17q21 containing BRCA1 was performed. YAC and cosmid contigs spanning the BRCA1 region were used to select cDNA clones from pools of cDNAs derived from human placenta, HeLa cells, activated T cells, and fetal head. A minimum set of 48 fragments of nonoverlapping cDNAs that unequivocally mapped within a 1-Mb region was identified, although it is not yet known how many of these are derived from the same transcript. DNA sequence analyses revealed that 4 of these cDNAs were derived from known genes (EDH17B2, glucose-6-phosphatase, IAI.3B, and E1AF), 1 is a member of a previously described gene family (HMG-17), and 7 share substantial identity with previously described genes from human or other species. The remainder showed no significant homology to known genes. Limited PCR-based expression profiles of a set of 13 of the genes were performed, and all gave positive results with at least some cDNA sources supporting the contention that they truly represent transcribed sequences. A comparison between genes obtained from this region by direct selection with those obtained by direct screening or exon trapping (see accompanying papers, this issue) revealed that over 90% of the genes identified by exon trapping were represented in the selected material and that at least two additional genes that appear to represent low abundance transcripts with restricted expression profiles were identified by selection but not by other means.

Construction of a transcription map surrounding the BRCA1 locus of human chromosome 17

We have used a combination of methods (exon amplification, direct selection, direct screening, evolutionary conservation, island rescue-PCR, and direct sequence analysis) to survey approximately 600 kb of genomic DNA surrounding the BRCA1 gene for transcribed sequences. We have cloned a set of fragments representing at least 26 genes. The DNA sequence of these clones reveals that 5 are previously cloned genes; the precise chromosomal location of 2 was previously unknown, and 3 have been cloned and mapped by others to this interval. Three other genes, including BRCA1 itself, have recently been mapped independently to this region. Sequences from 11 genes are similar but not identical matches to known genes; 5 of these appear to be the human homologues of genes cloned from other species. Another 7 genes have no similarity with known genes. In addition, 39 putative exons and 14 expressed sequence tags have been identified and mapped to individual cosmids. This transcript map provides a detailed description of gene organization for this region of the genome.

A YAC-, P1-, and cosmid-based physical map of the BRCA1 region on chromosome 17q21

A familial early-onset breast cancer gene (BRCA1) has been localized to chromosome 17q21. To characterize this region and to aid in the identification of the BRCA1 gene, a physical map of a region of 1.0-1.5 Mb between the EDH17B1 and the PPY loci on chromosome 17q21 was generated. The physical map is composed of a yeast artificial chromosome (YAC) and P1 phage contig with one gap. The majority of the interval has also been converted to a cosmid contig. Twenty-three PCR-based sequence-tagged sites (STSs) were mapped to these contigs, thereby confirming the order and overlap of individual clones. This complex physical map of the BRCA1 region was used to isolate genes by a number of gene identification techniques and to generate transcript maps of the region, as presented in the three accompanying manuscripts of Brody et al. (1995), Osborne-Lawrence et al. (1995), and Friedman et al. (1995).

BRCA1 mutations in primary breast and ovarian carcinomas

Loss of heterozygosity data from familial tumors suggest that BRCA1, a gene that confers susceptibility to ovarian and early-onset breast cancer, encodes a tumor suppressor. The BRCA1 region is also subject to allelic loss in sporadic breast and ovarian cancers, an indication that BRCA1 mutations may occur somatically in these tumors. The BRCA1 coding region was examined for mutations in primary breast and ovarian tumors that show allele loss at the BRCA1 locus. Mutations were detected in 3 of 32 breast and 1 of 12 ovarian carcinomas; all four mutations were germline alterations and occurred in early-onset cancers. These results suggest that mutation of BRCA1 may not be critical in the development of the majority of breast and ovarian cancers that arise in the absence of a mutant germline allele.

A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1

A strong candidate for the 17q-linked BRCA1 gene, which influences susceptibility to breast and ovarian cancer, has been identified by positional cloning methods. Probable predisposing mutations have been detected in five of eight kindreds presumed to segregate BRCA1 susceptibility alleles. The mutations include an 11-base pair deletion, a 1-base pair insertion, a stop codon, a missense substitution, and an inferred regulatory mutation. The BRCA1 gene is expressed in numerous tissues, including breast and ovary, and encodes a predicted protein of 1863 amino acids. This protein contains a zinc finger domain in its amino-terminal region, but is otherwise unrelated to previously described proteins. Identification of BRCA1 should facilitate early diagnosis of breast and ovarian cancer susceptibility in some individuals as well as a better understanding of breast cancer biology.