Differential expression of human HOX-2 genes along the anterior-posterior axis in embryonic central nervous system

Direct reprogramming of fibroblasts into neural stem cells by defined factors

Recent studies have shown that defined sets of transcription factors can directly reprogram differentiated somatic cells to a different differentiated cell type without passing through a pluripotent state, but the restricted proliferative and lineage potential of the resulting cells limits the scope of their potential applications. Here we show that a combination of transcription factors (Brn4/Pou3f4, Sox2, Klf4, c-Myc, plus E47/Tcf3) induces mouse fibroblasts to directly acquire a neural stem cell identity-which we term as induced neural stem cells (iNSCs). Direct reprogramming of fibroblasts into iNSCs is a gradual process in which the donor transcriptional program is silenced over time. iNSCs exhibit cell morphology, gene expression, epigenetic features, differentiation potential, and self-renewing capacity, as well as in vitro and in vivo functionality similar to those of wild-type NSCs. We conclude that differentiated cells can be reprogrammed directly into specific somatic stem cell types by defined sets of specific transcription factors.

Abnormal rib number in childhood malignancy: implications for the scoliosis surgeon

STUDY DESIGN

Retrospective review.

OBJECTIVE

To determine if rib anomalies are present in pediatric malignancies in the United States.

SUMMARY OF BACKGROUND DATA

Scoliosis surgeons view radiographs of the entire spine, counting the number of ribs. A European study noted that rib anomalies were more common in certain malignancies. We wished to determine if this is also true in the United States. If so, the potential for screening, early detection of malignancy, and a better understanding of tumor biology is possible.

METHODS

A retrospective review of 218 children with malignancy and a control group of 200 children with polytrauma or suspected child abuse was performed. Chest radiographs were reviewed to determine the number of ribs, and the presence of rib anomalies. 24 ribs was considered normal, <24 or >24 was considered abnormal. P < 0.05 was considered significant.

RESULTS

The average age was 6.8 +/- 5.5 years and number of ribs was 23.8 +/- 0.6. Rib number was normal in 86.8%. There were significant differences between the malignancy and control groups in age (control, 5.7 +/- 5.1 years; malignancy, 7.8 +/- 5.7 years, P = 0.00007), rib number (control, 23.9 +/- 0.5; malignancy, 23.7 +/- 0.7, P = 0.001), and normal/abnormal rib counts (control, 92% normal; malignancy, 82% normal, P = 0.003). In the malignant group, 50% had a lymphoproliferative malignancy, 33% a solid tumor, and 17.0% a neural tumor. Neural malignancies had a higher incidence of rib abnormalities compared with lymphoproliferative or solid malignancies (P = 0.01). Relative to the control group, those with a neural and lymphoproliferative malignancy were 6.23 (95% CI, 2.7-14.5) and 2.0 (95% CI, 1.0-4.1) times more likely to have an abnormal rib count.

CONCLUSIONS

Homeobox genes, important in vertebral and rib sequencing, are abnormally expressed in many different malignancies. This association is a question of great interest. What is the potential for rib number being used as a predictor of childhood malignancy? Can these findings be expanded to adults? These questions require further research. The association noted in this study is interesting but should not yet be used to alarm parents regarding an increased risk of malignancy in their children.

Homeobox genes in normal and malignant cells

Homeobox genes are transcription factors primarily involved in embryonic development. Several homeobox gene families have so far been identified: Hox, EMX, PAX, MSX as well as many isolated divergent homeobox genes. Among these, Hox genes are most intriguing for having a regulatory network structure organization. Recent indications suggest the involvement of homeobox genes in (i) crucial adult eukariotic cell functions and (ii) human diseases, spanning from diabetes to cancer. In this review we will discuss the mechanisms through which homeobox genes act, and will propose a model for the function of the Hox gene network as decoding system for achieving specific genetic programs. New technologies for whole-genome RNA expression will be crucial to evaluate the clinical relevance of homeobox genes in structural and metabolic diseases.

Deregulated expression of homeobox-containing genes, HOXB6, B8, C8, C9, and Cdx-1, in human colon cancer cell lines

Previously we have demonstrated a reciprocal deregulation of various homeobox genes (HOXB6, B8, C8 and C9 vs Cdx-1) in human colorectal cancer (CRC). In the present study, using RT-PCR, we have investigated the expression pattern of these homeobox genes in various human colon cell lines, representing various stages of colon cancer progression and differentiation. Thus, we have tested polyposis coli Pc/AA adenoma cells, Caco-2, HT-29 and LS174T adenocarcinoma cell lines. All cell lines, except LS174T, demonstrated a pattern of deregulated homeobox gene expression which resembled that of CRC. In contrast, the pattern of expression of these genes in the highly oncogenic LS174T cells, as well as in Caco-2 cells transfected with activated Ha-ras or Polyoma middle T oncogene, resembled that of the normal mucosa. The reciprocal deregulation of HOX and Cdx-1 genes in CRC and in CRC-derived cell lines suggests a possible role in human CRC development.

Localization of a gene for Duane retraction syndrome to chromosome 2q31

Duane retraction syndrome (DRS) is a congenital eye-movement disorder characterized by a failure of cranial nerve VI (the abducens nerve) to develop normally, resulting in restriction or absence of abduction, restricted adduction, and narrowing of the palpebral fissure and retraction of the globe on attempted adduction. DRS has a prevalence of approximately 0.1% in the general population and accounts for 5% of all strabismus cases. Undiagnosed DRS in children can lead to amblyopia, a permanent uncorrectable loss of vision. A large family with autosomal dominant DRS was examined and tested for genetic linkage. After exclusion of candidate regions previously associated with DRS, a genomewide search with highly polymorphic microsatellite markers was performed, and significant evidence for linkage was obtained at chromosome 2q31 (D2S2314 maximum LOD score 11.73 at maximum recombination fraction. 0). Haplotype analysis places the affected gene in a 17.8-cM region between the markers D2S2330 and D2S364. No recombinants were seen with markers between these two loci. The linked region contains the homeobox D gene cluster. Three of the genes within this cluster, known to participate in hindbrain development, were sequenced in affected and control individuals. Coding sequences for these genes were normal or had genetic alterations unlikely to be responsible for the DRS phenotype. Identifying the gene responsible for DRS may lead to an improved understanding of early cranial-nerve development.

Homeobox genes and cancer

Homeobox-containing genes are a family of regulatory genes encoding transcription factors that primarily play a crucial role during development. Several indications suggest their involvement in the control of cell growth and, when dysregulated, in oncogenesis. We will describe the implications, in tumor origin and evolution, of members of the homeobox gene families HOX, EMX, PAX, and MSX as well as of other divergent homeobox genes. We will also propose a model for the function of the HOX gene network in controlling cell identity to account for the involvement of some HOX genes in both normal development and oncogenesis.

Localization of distant urogenital system-, central nervous system-, and endocardium-specific transcriptional regulatory elements in the GATA-3 locus

We found previously that neither a 6-kbp promoter fragment nor even a 120-kbp yeast artificial chromosome (YAC) containing the whole GATA-3 gene was sufficient to recapitulate its full transcription pattern during embryonic development in transgenic mice. In an attempt to further identify tissue-specific regulatory elements modulating the dynamic embryonic pattern of the GATA-3 gene, we have examined the expression of two much larger (540- and 625-kbp) GATA-3 YACs in transgenic animals. A lacZ reporter gene was first inserted into both large GATA-3 YACs. The transgenic YAC patterns were then compared to those of embryos bearing the identical lacZ insertion in the chromosomal GATA-3 locus (creating GATA-3/lacZ "knock-ins"). We found that most of the YAC expression sites and tissues are directly reflective of the endogenous pattern, and detailed examination of the integrated YAC transgenes allowed the general localization of a number of very distant transcriptional regulatory elements (putative central nervous system-, endocardium-, and urogenital system-specific enhancers). Remarkably, even the 625-kbp GATA-3 YAC, containing approximately 450 kbp and 150 kbp of 5' and 3' flanking sequences, respectively, does not contain the full transcriptional regulatory potential of the endogenous locus and is clearly missing regulatory elements that confer tissue-specific expression to GATA-3 in a subset of neural crest-derived cell lineages.

A target of the HoxB5 gene from the mouse nervous system

An epitope-specific antibody against the protein product of the murine HoxB5 gene was used to select an enriched library of Hox target sequences. Genomic DNA was purified by immunoaffinity chromatography, using glutaraldehyde-cross-linked chromatin from CNS of mouse embryos at gestational day 15. Screening was done by colony hybridization with TAAT-containing oligonucleotides, filter DNA-protein binding, and gel mobility shift assay. Nucleotide sequencing identified a 910 bp DNA fragment, containing a consensus Antennapedia-like binding site, and identical in 640 bps at 3' end of the clone to the promoter of the SPI3 gene, which encodes a serine protease inhibitor protein [Sun, J., Rose, J.B. and Bird, P., J. Biol. Chem., 270 (1995) 16089-16096]. In situ hybridization experiments were performed to see if a correlation could be found between the expression patterns the SPI3 and the HoxB5 genes. Using a 120 bp cDNA fragment as probe, SPI3 expression was detected mainly in the CNS of 15 day mouse embryos, a pattern which is similar to that of the HoxB5 gene at this stage [Hogan, B.L., Holland, P.W. and Lumsden, A., Cell Diff. Dev., 25 Suppl. (1988) 39-44; Sakach, M. and Safaei, R., Int. J. Dev. Neurosci., 14 (1996) 567-573]. In conclusion, data presented here suggest that the SPI3 gene is a candidate target of the HoxB5 gene in vertebrate embryos.

Homeobox genes: molecular link between congenital anomalies and cancer

Homeobox-containing genes play a major role in the control of segmental identity during embryonic development in Drosophila. Abnormalities of these genes have been shown to produce a wide variety of congenital anomalies in invertebrates and in vertebrates. Many transgenic mice, which are mutant for homeobox genes, show a specific skeletal abnormality, similar to the human cervical rib. In humans, a relationship exists between malformations and tumours. Human cervical rib has been shown to be associated with an increased incidence of malignancy. Recent evidence indicates that homeobox genes might also play a role in carcinogenesis. In this article, we explore the possibility that alterations of homeobox genes might be the basic underlying aetiology for the association between congenital malformations and tumours, at least in a proportion of cases. We provide evidence in support of this argument and suggest areas of further research which would confirm this concept.

Human colorectal carcinogenesis is associated with deregulation of homeobox gene expression

In the present study, the possible involvement of homeobox-containing genes in colorectal cancer (CRC) development was investigated. Using a stepwise screening approach and RT-PCR, we have demonstrated that the human HOXB6, B8, C8 and C9 are overexpressed at various stages of CRC. In contrast, all CRC cases exhibited a marked decrease in the homeodomain-containing Cdx1 gene expression. Recent data which suggest a regulatory link between HOXB8 and several tumor suppressor genes, such as DCC, APC, and TGF beta, sustain a possible implication of homeobox genes in colon carcinogenesis. Moreover, our data showing a decrease in Cdx1 expression are consistent with the notion that genes functioning in the establishment and maintenance of the intestinal epithelium might, upon deregulation, disturb the normal control of cellular proliferation, differentiation, and death, thus leading to cancer development.

PCR-survey of Hox-genes of the zebrafish: new sequence information and evolutionary implications

We analyzed the Hox gene complement of the zebrafish Danio rerio using a PCR survey. We found 18 new zebrafish HOM/Hox type sequences and one sequence of the msh group. For groups 1-3 and 8-10 we could unambiguously assign the zebrafish fragments to cognate groups. The assignment for cognate groups 4-7 had to remain tentative due to insufficient sequence variation. The number of zebrafish Hox fragments classified as members of cognate groups 1-4, 8, and 9 is identical to the number of genes in corresponding cognate groups of the mouse and human genomes. We found only two differences between the zebrafish and mouse Hox gene complement: four putative genes in group 10 (three in mammals) and only seven in the medial groups 5 to 7 (eight in mammals). Together with the previously published Hox gene sequences of the killifish, the larger number of zebrafish genes in group 10 is positive evidence for variation in the Hox gene complements among bony fish. In contrast, the Hox gene complement appears to be highly conserved among all tetrapods.

Expression of homebox-containing genes in human preimplantation development and in embryos with chromosomal aneuploidies

PURPOSE

The purpose of the study was to investigate homeobox gene expression in human oocytes and preembryos and in postimplantation embryos with impaired embryonic development determined by chromosomal abnormalities.

METHODS

Reverse transcriptase-polymerase chain reaction (RT-PCR) with intron spanning primer sets for Homeobox gene sequences was used.

RESULTS

The homeobox genes HoxA4, HoxA7, HoxB4, and HoxB5 were present in human oocytes and cleaving normal and triploid embryos. The expression pattern was different between chromosomally abnormal and normal first-trimester embryos. Of four homeobox transcripts (HoxA7, HoxB4+ ++, HoxB5, and HoxC6) that are expressed in diploid embryos, only HoxA7, HoxB4 and HoxC6 were present in a trisomy 7 embryo, and only HoxB4 and HoxB 5 in triploid embryos and an embryo with trisomy 9. Cloning experiments revealed differences in the number of homeobox clones obtained from trisomy 7 and control embryos.

CONCLUSIONS

The transcripts of homeobox genes, HoxA4, HoxA7, HoxB4, and HoxB5, were present in oocytes and cleaving embryos. The pattern of expression of homeobox genes in cultured fibroblasts derived from spontaneously aborted embryos with aneuploidies was different from that in control diploid cells.

The 5'-sequence of the murine Hox-b3 (Hox-2.7) gene and its intron contain multiple transcription-regulatory elements

We sought to clone and characterize the murine Hox-b3 gene. In Xenopus embryos, the homologous gene has been shown to be responsive to retinoic acid, an agent which has profound effects on tissue growth and development. By plaque hybridization, using a partial, murine Hox-b3 cDNA as a probe, we screened a genomic library and isolated a series of overlapping clones. Restriction fragments from positive clones were sequenced by the dideoxy method on an automated DNA sequencer. We report the genomic sequence of the murine Hox-b3 gene. The sequence has been submitted to the GenBank database (accession number U02278). Our sequence extends from the P1 promoter through the coding sequence of the gene to the 3'-untranslated region. In common with other homeobox genes, there is an intron between the conserved hexapeptide and the homeobox. It is 866 bp long and has 3'- and 5'-splice sites very similar to the consensus, a long polypyrimidine tract and a potential branch point near the 3'-splice site. We have analyzed the sequence 5' to the initiation codon and the intron for putative control elements, and have identified a series of putative transcription factor binding sites in the P1 promoter and intron, including two for the retinoid X receptor-beta. Their possible significance is discussed. The sequences we have identified may be responsible for the observed pattern of expression of the gene. This sequence and the clones from which it is derived will enable a molecular dissection of the P1 promoter region.

HOX gene expression in human small-cell lung cancers xenografted into nude mice

Transcription factors are crucial to an understanding of the molecular basis of neoplasia. Homeobox-containing genes are a family of transcriptional regulators encoding DNA-binding homeodomains, involved in the control of normal development. Class-I human homeobox-containing genes (HOX genes) display a peculiar chromosomal organization, perhaps directly related to their function. Aberrant expression of homeobox-genes has been associated with both morphological abnormalities and oncogenesis. We have recently observed that alterations in HOX gene expression are detectable in kidney and colon cancer when compared to the corresponding normal organs. Here we have analyzed the expression of HOX genes in primary and metastatic human small-cell lung cancer (SCLC) xenografted in nude mice, in order to investigate whether HOX gene expression correlates with the histology and stage of SCLC progression. The results show that different SCLCs display differential patterns of HOX gene expression. Furthermore, in SCLC, the number of actively expressed HOX genes might be substantially lower in metastatic cancers than in primary tumors. The alteration in HOX gene expression in SCLCs mainly concerns the HOX B and C loci. This finding suggests that downregulation of HOX genes may play a role in small-cell lung cancer progression, possibly through their implication in tumor suppression.

Coordinate expression and proliferative role of HOXB genes in activated adult T lymphocytes

We investigated the expression of HOXB cluster genes in purified phytohemagglutinin (PHA)-activated T lymphocytes from normal adult peripheral blood by reverse transcription PCR and RNase protection. These genes are not expressed in quiescent T cells, except for barely detectable B1 RNA. After the PHA stimulus, HOXB gene activation initiates coordinately as a rapid induction wave in the 3'-->5' cluster direction (i.e., from HOXB1 through B9 genes). Thus, (i) expression of the foremost 3'-located B1 and B2 genes peaks 10 min after PHA addition and then rapidly declines, (ii) activation of B3, B4, and B5 begins 10 min after PHA addition and peaks at later times (i.e., at 120 min for B5), (iii) B6, B7, and B9 are expressed at a low level starting at later times (45 to 60 min), and (iv) B8 remains silent. Treatment of PHA-activated T lymphocytes with antisense oligonucleotides to B2 or B4 mRNA causes a drastic inhibition of T-cell proliferation and a decreased expression of T-cell activation markers (i.e., interleukin 2 and transferrin receptors). Similarly, treatment of CEM-CCRF, Peer, and SEZ627 T acute lymphocytic leukemia cell lines with anti-B4 oligomer markedly inhibits cell proliferation. Finally, T cells stimulated by a low dosage of PHA in the presence of 1 microM retinoic acid show a marked increase of both HOXB expression, particularly B2, and cell proliferation. These studies provide novel evidence on the role of HOX genes in adult cell proliferation. (i) Coordinate, early activation of HOXB genes from the 3'-->5' cluster side apparently underlies T-cell activation. (ii) The expression pattern in adult PHA-activated T cells is strikingly similar to that observed in retinoic acid-induced teratocarcinoma cells (A. Simeone, D. Acampora, L. Arcioni, P. W. Andres, E. Boncinelli, and F. Mavilio, Nature (London) 346:763-766, 1990), thus suggesting that molecular mechanisms underlying HOX gene expression in the earliest stages of development may also operate in activated adult T lymphocytes.

Coordinate expression and proliferative role of HOXB genes in activated adult T lymphocytes

We investigated the expression of HOXB cluster genes in purified phytohemagglutinin (PHA)-activated T lymphocytes from normal adult peripheral blood by reverse transcription PCR and RNase protection. These genes are not expressed in quiescent T cells, except for barely detectable B1 RNA. After the PHA stimulus, HOXB gene activation initiates coordinately as a rapid induction wave in the 3'-->5' cluster direction (i.e., from HOXB1 through B9 genes). Thus, (i) expression of the foremost 3'-located B1 and B2 genes peaks 10 min after PHA addition and then rapidly declines, (ii) activation of B3, B4, and B5 begins 10 min after PHA addition and peaks at later times (i.e., at 120 min for B5), (iii) B6, B7, and B9 are expressed at a low level starting at later times (45 to 60 min), and (iv) B8 remains silent. Treatment of PHA-activated T lymphocytes with antisense oligonucleotides to B2 or B4 mRNA causes a drastic inhibition of T-cell proliferation and a decreased expression of T-cell activation markers (i.e., interleukin 2 and transferrin receptors). Similarly, treatment of CEM-CCRF, Peer, and SEZ627 T acute lymphocytic leukemia cell lines with anti-B4 oligomer markedly inhibits cell proliferation. Finally, T cells stimulated by a low dosage of PHA in the presence of 1 microM retinoic acid show a marked increase of both HOXB expression, particularly B2, and cell proliferation. These studies provide novel evidence on the role of HOX genes in adult cell proliferation. (i) Coordinate, early activation of HOXB genes from the 3'-->5' cluster side apparently underlies T-cell activation. (ii) The expression pattern in adult PHA-activated T cells is strikingly similar to that observed in retinoic acid-induced teratocarcinoma cells (A. Simeone, D. Acampora, L. Arcioni, P. W. Andres, E. Boncinelli, and F. Mavilio, Nature (London) 346:763-766, 1990), thus suggesting that molecular mechanisms underlying HOX gene expression in the earliest stages of development may also operate in activated adult T lymphocytes.

Vertebrate homeobox genes

In the former part of the review the principal available data about Hox genes, their molecular organisation and their expression in vertebrate embryos, with particular emphasis for mammals, are briefly summarized. In the latter part we analysed the expression of four mouse homeobox genes related to two Drosophila genes expressed in the developing head of the fly: Emx1 and Emx2, related to ems, and Otx1 and Otx2, related to otd.

Hox homeobox genes and regionalisation of the nervous system

The Hox family of homeobox-containing genes are intimately associated with the processes of axial patterning in vertebrate embryos. This family of transcription factors is widely conserved in evolution and by analogy with their Drosophila counterparts, the HOM-C homeotic genes, may play a role in establishing regional identity in a number of embryonic systems, including the CNS. The patterns of expression of these genes are linked with the generation of rhombomeres and neural crest in the developing hindbrain, and suggest that they provide a molecular system for generating a combinatorial patterning mechanism. Analysis of mouse Hox mutants generated by homologous recombination have clearly demonstrated that the genes have important roles in normal regionalisation of the hindbrain and branchial arches, and this has lead to interest in how their early patterns are established in the nervous system. The Hox genes and their relation to hindbrain segmentation therefore provide a means of examining the cascade of events which regulates pattern formation in early neural development.

Mouse Hox genetic functions

Functional analysis of the genetic roles of the mammalian Hox homeobox family has not been facilitated by the analysis of disease-associated or classically derived mutant loci. However, an increasing number of mouse Hox mutations, generated by homologous recombination, have now demonstrated that the Hox genes are key components in regulating the patterning of axial structures.

Identification of a retinoic acid responsive enhancer 3' of the murine homeobox gene Hox-1.6

The putative vertebrate morphogen retinoic acid (RA) has been shown to induce expression of many mammalian homeobox genes in cell lines, suggesting expression of this gene family in developing vertebrate embryos may be controlled in part by RA. Using the teratocarcinoma cell line F9 as a model system, we have studied the RA-response of the murine homeobox gene Hox-1.6. RA treatment of F9 cells causes the appearance of a DNAse I hypersensitive site 3' of Hox-1.6, approximately 5 kb downstream of the Hox-1.6 promoter, and this site has been shown to reflect the presence of an RA-responsive enhancer 3' of the gene. The RA-responsiveness of the enhancer is controlled by a retinoic acid responsive element (RARE) identical to the RARE of the retinoic acid receptor (RAR) beta gene; however, other sequences also influence the activity of the enhancer, suggesting the presence of binding sites for novel proteins which regulate Hox-1.6 expression. Experiments with Hox-1.6 minigenes in which lacZ expression is controlled by the Hox-1.6 promoter and enhancer demonstrate that it is the 3' enhancer which confers RA responsiveness on the endogenous promoter, as constructs which lack the enhancer, or the RARE alone, do not respond to RA. Our results support the idea that RA is an endogenous vertebrate morphogen; identification of the RA-responsive enhancer downstream of Hox-1.6 demonstrates that RA directly controls the transcription of at least one member of a gene family that determines tissue identity in the vertebrate embryo.

Homeobox-containing genes in the newt are organized in clusters similar to other vertebrates

In vertebrates, the majority of homeobox (HBox) genes are found in four clusters and this structural organization is believed to be of functional importance. Many HBox genes sustain their expression in the appendages of the adult newt. To further understand their regulation, the genomic loci of four newt HBox genes (two from the human HBox (HOX)-2 complex and two from the HOX-3 complex) were analysed and compared with homologous loci in other vertebrates. Notophthalmus viridescens HBox (NvHBox) genes were selected from a lambda EMBL3 library and analysed by restriction mapping and nucleotide (nt) sequencing. The nt sequences of the NvHBox genes have a very high degree of homology (more than 90%) with the human and mouse HBox genes, HOX-3.3, HOX-3.4, HOX-2.7 and HOX-2.8. The sequences flanking the HBox are also very homologous to their human and mouse counterparts. Moreover, the size of the DNA spacer separating NvHBox-3.3 from NvHBox-3.4, and NvHBox-2.7 from NvHBox-2.8 in the newt is similar in the homologous regions of the mouse and human, despite there being a C value ten times greater in the newt genome. Finally, three of these NvHBox genes are expressed in the limbs of the adult newt.

Neuropathologic findings in cortical resections (including hemispherectomies) performed for the treatment of intractable childhood epilepsy

Despite the use of hemispherectomy in the treatment of medically refractory seizures since the early 1950's, few studies published have documented neuropathologic findings in the resected specimens. This report describes the neuropathologic findings in 38 children who underwent either hemispherectomy or multilobar cortical resection as treatment for medically intractable epilepsy between 1986 and 1990. Examination of the resected specimens revealed a variety of abnormalities which fell into four broad categories. Malformations or hamartomatous lesions were the dominant finding in 15 patients, whereas encephalomalacic lesions were the most prominent abnormality in 16; chronic pathogen-free encephalitits (Rasmussen's encephalitis) was present in 3 and an additional 3 children had Sturge-Weber-Dimitri syndrome. There were no gross or microscopic abnormalities in 1 patient. This report provides the first comprehensive description of the pathologic findings in a series of children with refractory epilepsy of varying types treated by hemispherectomy-multilobar resection.

Multiple spatially specific enhancers are required to reconstruct the pattern of Hox-2.6 gene expression

Murine Hox genes are organized into four clusters that share many features with the homeotic clusters of Drosophila. This evolutionary conservation and the clear relationships between the position of a gene within a cluster and its expression pattern have led to the suggestion that the structure of the cluster is essential for proper regulation. Using a Hox-2.6-lacZ reporter gene in transgenic mice we have shown that the overall expression pattern of the endogenous Hox-2.6 gene can be reconstructed when it is isolated from the complex. The transgene was expressed in the proper tissues, with the correct spatial distribution and temporal pattern. Furthermore, direct comparison by in situ hybridization revealed that the levels of transgene expression are similar to those of the endogenous gene. This has allowed us to define three elements that regulate particular aspects of the Hox-2.6 pattern, two of which act as spatially specific enhancers. One enhancer, region A, directed expression only in the neural tube, whereas the other, region C, specified the majority of the Hox-2.6 pattern. Both were also capable of imposing the correct boundaries of expression on heterologous promoters. The definition of such elements will allow the characterization of the trans-acting factors that mediate spatial regulation in the mammalian embryo.

The expression of murine Hox-2 genes is dependent on the differentiation pathway and displays a collinear sensitivity to retinoic acid in F9 cells and Xenopus embryos

In this paper we describe experiments that detail the response of murine Hox-2 genes to cellular differentiation and retinoic acid in cell culture. Hox-2 genes are transiently activated in differentiating ES cells even in the absence of retinoic acid (RA), indicating that their induction is a normal aspect of differentiation. Furthermore, in the continuous presence of RA F9 teratocarcinoma cells show a differential ability to maintain Hox-2 expression depending upon whether the cells follow a visceral or parietal endoderm pathway. These data suggest a clear dependence of Hox-2 expression on the degree and type of differentiation in different cells. However, RA also has dramatic differentiation independent effects on Hox-2 regulation. In ES cells the levels of Hox expression are greatly enhanced by exposure to RA, and in F9 cells of the visceral or parietal phenotype the continuous presence of RA is required to maintain these high levels. Nuclear run-on experiments illustrate that Hox-2 genes are active in F9 stem cells and that a large portion of the RA induction is mediated by post-transcriptional mechanisms. Therefore RA exerts its effects on Hox-2 expression by upregulating or modulating genes which are already active, rather than by turning-on silent genes. All nine Hox-2 genes are induced in F9 cells by RA and there is a direct correlation (collinearity) between gene order and the relative dose response of each gene to RA. In Xenopus embryos treated with RA, homologues of the Hox-2 genes also displayed a temporal and dose response collinearity with gene organisation. Together these findings suggest that the collinear response to RA is highly conserved in vertebrates and combined with the ability of RA to modify expression during cellular differentiation could be an important feature of the Hox-2 cluster itself used to generate the spatially-restricted patterns of gene expression in embryogenesis.

HOX gene activation by retinoic acid

Vertebrate homeobox genes of the Hox family are, like Drosophila homeotic genes, organized in gene clusters and show a strict correspondence, or collinearity, between the order of the genes (3' to 5') within the chromosomal cluster and that of their expression domains (anterior to posterior) in the embryo. Recent data obtained from embryonal carcinoma cells induced to differentiate by retinoic acid cast some light on the molecular mechanisms underlying the collinear expression of the Hox genes.

Relationship of eukaryotic DNA replication to committed gene expression: general theory for gene control

The historic arguments for the participation of eukaryotic DNA replication in the control of gene expression are reconsidered along with more recent evidence. An earlier view in which gene commitment was achieved with stable chromatin structures which required DNA replication to reset expression potential (D. D. Brown, Cell 37:359-365, 1984) is further considered. The participation of nonspecific stable repressor of gene activity (histones and other chromatin proteins), as previously proposed, is reexamined. The possible function of positive trans-acting factors is now further developed by considering evidence from DNA virus models. It is proposed that these positive factors act to control the initiation of replicon-specific DNA synthesis in the S phase (early or late replication timing). Stable chromatin assembles during replication into potentially active (early S) or inactive (late S) states with prevailing trans-acting factors (early) or repressing factors (late) and may asymmetrically commit daughter templates. This suggests logical schemes for programming differentiation based on replicons and trans-acting initiators. This proposal requires that DNA replication precede major changes in gene commitment. Prior evidence against a role for DNA replication during terminal differentiation is reexamined along with other results from terminal differentiation of lower eukaryotes. This leads to a proposal that DNA replication may yet underlie terminal gene commitment, but that for it to do so there must exist two distinct modes of replication control. In one mode (mitotic replication) replicon initiation is tightly linked to the cell cycle, whereas the other mode (terminal replication) initiation is not cell cycle restricted, is replicon specific, and can lead to a terminally differentiated state. Aberrant control of mitotic and terminal modes of DNA replication may underlie the transformed state. Implications of a replicon basis for chromatin structure-function and the evolution of metazoan organisms are considered.

CHox E, a chicken homeogene of the H2.0 type exhibits dorso-ventral restriction in the proliferating region of the spinal cord

CHox E is a novel chicken homeogene that belongs to the H2.0 family of homeodomains. Its homeobox sequence is interrupted by an intron between amino acids 44 and 45. Expression of CHox E during embryogenesis is localized to the central nervous system. The anterior boundary of CHox E expression can initially be localized to rhombomere number 1, later in development this boundary reaches up to the rhombencephalic isthmus. CHox E expression in the spinal cord localizes dorso-ventrally to the dorsal half of the basal plate. CHox E expression is always restricted to the proliferating region, the ventricular zone. As the ventricular zone becomes restricted laterally, so does the CHox E expressing region. Once this region of the ventricular zone ceases to exist, CHox E specific transcripts become undetectable. The site and time of CHox E expression suggest a very early function in the differentiation of the cells derived from that region of the ventricular zone.

EVX2, a human homeobox gene homologous to the even-skipped segmentation gene, is localized at the 5' end of HOX4 locus on chromosome 2

We isolated and mapped three new human homeoboxes located on chromosome 2 upstream from the reported seven HOX4 homeobox sequences. Two of them, HOX41 and HOX4H, clearly belong to the HOX gene family, in particular to homology groups 1 and 2, and possibly represent the most 5' HOX4 homeoboxes. A third homeobox 13 kb upstream from HOX41 was identified. Sequencing data show that this is the human homolog of the murine Evx-2 homeobox. Both homeoboxes are closely related to the murine Evx-1 and to the frog Xhox-3 homeoboxes. The four genes represent vertebrate homologs of Drosophila even-skipped (eve), a segmentation gene of the pair-rule class. Human EVX2 sequences belong to an active gene because they are transcribed and properly processed in cells and tissues. We have identified for the first time a homeogene of a different class at a HOX locus. These findings are relevant to the understanding of the evolution of HOX gene clusters and their regulation.

Differential regulation by retinoic acid of the homeobox genes of the four HOX loci in human embryonal carcinoma cells

We studied the expression of 38 human homeobox genes belonging to the four HOX complex loci in embryonal carcinoma (EC) cells induced to differentiate by culturing them in a medium containing retinoic acid (RA). Genes located at the 3' end of each one of the four HOX loci are activated by RA in a sequential order colinear with their 3' to 5' arrangement in the cluster: 3' HOX genes respond early to the drug while upstream genes respond progressively later. Among the genes located at the 5' end of HOX loci RNase protection analysis reveals that one HOX3 gene and four HOX4 genes are weakly expressed in EC stem cells and downregulated upon treatment with 10(-5) M RA. While activation of early responding genes does not require continuous protein synthesis, the observed timing and polarity of gene activation is disrupted in the absence of protein synthesis.

A dominant negative mutation of the alpha retinoic acid receptor gene in a retinoic acid-nonresponsive embryonal carcinoma cell

Pluripotential embryonal carcinoma cells such as those of the P19 line differentiate when exposed to retinoic acid (RA). The RAC65 cell line is a mutant clone of P19 cells selected to be RA nonresponsive. RAC65 cells carry a rearrangement affecting one of the genes encoding a nuclear retinoic acid receptor (RAR alpha). The mutant gene encodes a protein, RAR alpha', that has lost its 70 C-terminal amino acids, thus truncating the RA-binding domain. The RAR alpha' was found to be a dominant repressor of transcription from an RA-responsive target gene; however, expression of RAR alpha' was insufficient to confer RA nonresponsiveness, suggesting that RAC65 cells carry an additional mutation(s) affecting RA-induced genes.

A dominant negative mutation of the alpha retinoic acid receptor gene in a retinoic acid-nonresponsive embryonal carcinoma cell

Pluripotential embryonal carcinoma cells such as those of the P19 line differentiate when exposed to retinoic acid (RA). The RAC65 cell line is a mutant clone of P19 cells selected to be RA nonresponsive. RAC65 cells carry a rearrangement affecting one of the genes encoding a nuclear retinoic acid receptor (RAR alpha). The mutant gene encodes a protein, RAR alpha', that has lost its 70 C-terminal amino acids, thus truncating the RA-binding domain. The RAR alpha' was found to be a dominant repressor of transcription from an RA-responsive target gene; however, expression of RAR alpha' was insufficient to confer RA nonresponsiveness, suggesting that RAC65 cells carry an additional mutation(s) affecting RA-induced genes.

Expression of HOX homeogenes in human neuroblastoma cell culture lines

Mammalian genes containing a class-I homeobox (HOX genes) are highly expressed in the embryonic nervous system. As a first step towards the molecular analysis of the role these genes play in neural cells, we studied the expression of four human HOX genes in five neuroblastoma (NB) cell lines - SK-N-BE, CHP-134, IMR-32, SK-N-SH and LAN-1 - during the process of differentiation induced by treatment with retinoic acid (RA). The four genes, HOX1D, 2F, 3E and 4B, located at corresponding positions in the four HOX loci, share a high degree of sequence similarity with the Drosophila Deformed homeotic gene and constitute a homology group, group 10. One of these genes, HOX1D, is not expressed in the cells used, whereas the other three are highly expressed in untreated and RA-induced NB cells, even though the expression pattern in the various lines is slightly different for the three genes. Our analysis reveals a complex and specific expression pattern in these lines, paving the way to an identification of different NB-cell populations by means of specific HOX gene expression schemes. On the other hand, in every line studied, morphological maturation toward a neuronal differentiated phenotype appears to be associated with increased HOX gene expression.

Sequential activation of HOX2 homeobox genes by retinoic acid in human embryonal carcinoma cells

RETINOIC acid had been implicated as a natural morphogen in chicken and frog embryogenesis, and is presumed to act through the gene regulatory activity of a family of nuclear receptors. Homeobox genes, which specify positional information in Drosophila and possibly in vertebrate embryogenesis, are among the candidate responsive genes. We previously reported that retinoic acid specifically induces human homeobox gene (HOX) expression in the embryonal carcinoma cell line NT2/D1. We now show that the nine genes of the HOX2 cluster are differentially activated in NT2/D1 cells exposed to retinoic acid concentrations ranging from 10(-8) to 10(-5) M. Genes located in the 3' half of the cluster are induced at peak levels by 10(-8) M retinoic acid, whereas a concentration of 10(-6) to 10(-5) M is required to fully activate 5' genes. At both high and low retinoic acid concentrations, HOX2 genes are sequentially activated in embryonal carcinoma cells in the 3' to 5' direction.

Molecular mechanisms underlying the expression of the human HOX-5.1 gene

The complex mechanisms underlying homeobox genes expression involve regulation at transcriptional, post-transcriptional and translational levels. The multiple transcripts of the human HOX-5.1 gene are expressed differentially in tissue- and stage-specific patterns during embryogenesis, and differentially induced by retinoic acid (RA) in human embryonal carcinoma (EC) NT2/D1 cells. We have sequenced 6.3 Kb of the genomic region containing the HOX-5.1 gene and analyzed its mechanisms of expression. Two alternative promoters underlie the transcription of two classes of HOX-5.1-specific mRNAs. These classes differ in tissue and subcellular distribution, induction by RA, structure of the 5'-UT region and mRNA stability: these features are compatible with a differential function of the two classes of transcripts in embryogenesis.

Human HOX genes are differentially activated by retinoic acid in embryonal carcinoma cells according to their position within the four loci

We studied the expression of 33 human homeobox genes belonging to four complex HOX loci in embryonal carcinoma NT2/D1 cells. These cells can be induced to differentiate by culturing them in media containing retinoic acid. Northern blot analysis reveals that no expression of these genes was detectable in NT2/D1 stem cells, whereas 22 HOX genes are well expressed in NT2/D1 cells treated with 10 microM retinoic acid for 14 days. The 11 HOX genes the expression of which remained undetectable in NT2/D1 cells after this treatment are located at the 5' end of their loci: four in HOX1, five in HOX3 and two in HOX4. The boundary between induced and silent genes roughly corresponds to the HOX genes constituting the homology group 5, related to the Abdominal-B homeotic gene of Drosophila. All nine identified HOX2 genes are well expressed in fully induced NT2/D1 cells and none of them maps 5' genes of this homology group. We conclude that HOX genes are differentially activated by retinoic acid in these cells according to their physical location within the four chromosomal loci.

A yeast artificial chromosome containing the mouse homeobox cluster Hox-2

We have isolated two genes, Hox-2.8 and Hox-2.9, from the mouse homeobox cluster Hox-2, located on chromosome 11. A 120-kilobase yeast artificial chromosome (YAC) containing a large region of the murine Hox-2 cluster, including 45 kilobases of sequence upstream of the most 5' gene, was cloned. The DNA sequence of the YAC is unrearranged relative to the genomic map. We have subcloned from the YAC insert a homeobox gene, Hox-2.8, whose homeodolmain is highly related to that of the Drosophila homeotic gene proboscopedia (pb). The expression pattern of Hox-2.8 during embryogenesis extends the trend established by genes from Hox-2.5 to -2.7 of successively anterior domains of expression in the neural tube. We have also subcloned and sequenced from a cosmid the labial (lab)-related Hox-2.9, the most 3' member of the cluster to date. These data lend further support to the idea of a common evolutionary origin of the mouse Hox and Drosophila HOM clusters. The YAC will enable us to construct modified forms of the Hox-2 cluster in yeast and to identify their effect on the phenotype of the animal in transgenic mouse strains.

Region-specific enhancers near two mammalian homeo box genes define adjacent rostrocaudal domains in the central nervous system

To gain insight to the mechanisms underlying region-specific gene expression in mammalian development, we investigated the regulatory DNA associated with the proximal promoter of two homeo box genes, murine Hox-1.3 and human Hox-5.1. Using lacZ gene fusions in transgenic mice, we identified regulatory elements in the 5'-flanking sequences of the Hox-1.3 and the Hox-5.1 genes that specifically direct beta-galactosidase expression to the brachial and the upper cervical regions (respectively) of the central nervous system (CNS). These two elements act at the transcriptional level, are active in either orientation, and confer region-specific expression to unrelated promoters, satisfying the criteria for enhancer elements. The two spatial domains defined by these enhancers are directly adjoining, extend along the rostrocaudal axis for the same span of 6-7 metameres, and represent specific subsets of the overall CNS regions expressing all endogenous Hox-1.3 or Hox-5.1 transcripts. The adjacent domains in the developing murine CNS that express Hox-1.3 and Hox-5.1 gene fusions are strikingly reminiscent of the adjacent stripes of expression in Drosophila embryos seen with Sex combs reduced and Deformed, the two Drosophila homeotic genes most homologous to Hox-1.3 and Hox-5.1, respectively. These findings represent the first demonstration of region-specific mammalian enhancers and raise the possibility that the mammalian CNS may be subdivided into a series of rostrocaudal domains on the basis of the activity of enhancers near homeo box genes.