Molecular cloning, sequencing and expression of the mRNA encoding human Cdx1 and Cdx2 homeobox. Down-regulation of Cdx1 and Cdx2 mRNA expression during colorectal carcinogenesis

Defining the molecular mechanisms involved in cancer formation and progression is still a major challenge in colorectal-cancer research. Our strategy was to characterize genes whose expression is altered during colorectal carcinogenesis. To this end, the phenotype of a colorectal tumour was previously established by partial sequencing of a large number of its transcripts and the genes of interest were selected by differential screening on high-density filters with mRNA of colorectal cancer and normal adjacent mucosa. Fifty-one clones were found over-expressed and 23 were underexpressed in the colorectal-cancer tissues of the 5 analyzed patients. Among the latter, clones 6G2 and 32D6 were found of particular interest, since they had significant homology with several homeodomain-containing genes. The highest degree of similarity was with the murine Cdx1 for 6G2, and with the murine Cdx2 and hamster Cdx3 for 32D6. Using a RT-PCR approach, complete sequence of both types of homeobox-containing cDNA was obtained. The amino-acid sequence of the human Cdx1 is 85% identical to the mouse protein, and human Cdx2 has 94% identity with the mouse Cdx2 and hamster Cdx3. Tissue-distribution analysis of Cdx1 and Cdx2 mRNA showed that both transcripts were specifically expressed in small intestine, in colon and rectum. Twelve tissue samples from colorectal adenocarcinomas and the corresponding normal mucosa were analyzed by Northern blot. Expression of the 2 types of mRNA was either reduced or absent in 10 of them. Several colon-cancer cell lines were also analyzed. Cdx2 mRNA was absent from LS174T cells and Cdx1 mRNA was absent in PF11, TC7 and SW480 cells; none was detected in HT29 cells. It was concluded that decrease in human Cdx1 and/or Cdx2 expression is associated with colorectal tumorigenesis.

Molecular cloning, sequencing and expression of the mRNA encoding human Cdx1 and Cdx2 homeobox. Down-regulation of Cdx1 and Cdx2 mRNA expression during colorectal carcinogenesis

Defining the molecular mechanisms involved in cancer formation and progression is still a major challenge in colorectal-cancer research. Our strategy was to characterize genes whose expression is altered during colorectal carcinogenesis. To this end, the phenotype of a colorectal tumour was previously established by partial sequencing of a large number of its transcripts and the genes of interest were selected by differential screening on high-density filters with mRNA of colorectal cancer and normal adjacent mucosa. Fifty-one clones were found over-expressed and 23 were underexpressed in the colorectal-cancer tissues of the 5 analyzed patients. Among the latter, clones 6G2 and 32D6 were found of particular interest, since they had significant homology with several homeodomain-containing genes. The highest degree of similarity was with the murine Cdx1 for 6G2, and with the murine Cdx2 and hamster Cdx3 for 32D6. Using a RT-PCR approach, complete sequence of both types of homeobox-containing cDNA was obtained. The amino-acid sequence of the human Cdx1 is 85% identical to the mouse protein, and human Cdx2 has 94% identity with the mouse Cdx2 and hamster Cdx3. Tissue-distribution analysis of Cdx1 and Cdx2 mRNA showed that both transcripts were specifically expressed in small intestine, in colon and rectum. Twelve tissue samples from colorectal adenocarcinomas and the corresponding normal mucosa were analyzed by Northern blot. Expression of the 2 types of mRNA was either reduced or absent in 10 of them. Several colon-cancer cell lines were also analyzed. Cdx2 mRNA was absent from LS174T cells and Cdx1 mRNA was absent in PF11, TC7 and SW480 cells; none was detected in HT29 cells. It was concluded that decrease in human Cdx1 and/or Cdx2 expression is associated with colorectal tumorigenesis.

Modulation of mRNA levels in the presence of thymocytes and genome mapping for a set of genes expressed in mouse thymic epithelial cells

Modulation of gene expression in mouse thymic epithelium upon culture in the presence of thymocytes (coculture) was studied by comparison of hybridization signatures on a set of nearly 5000 mouse thymus cDNA clones. Forty-nine differentially expressed clones (usually down-regulated in coculture) were characterized by tag sequencing. Many of them corresponded to entities that had not been described previously in the mouse, and were further characterized by genome mapping. This set of genes appears to be involved in growth regulation and differentiation within the thymus.

Differential mRNA expression in untreated and TNF-alpha elicited murine dendritic cells precursors

We have compared the pattern of gene expression in long term cultured precursor dendritic cells (DC), either untreated (immature) or cultured for two days in the presence of recombinant murine (rm)-TNF alpha (mature). The hybridization signature of complex cDNA probes prepared from total RNA extracted from immature and mature DC were analyzed using a mouse thymic cDNA library, gridded on high density filters. For each clone spotted on the filters, we have measured using an imaging plate device the hybridization signals of the complex probe obtained from immature or mature DC. Comparative analysis of these values allowed us to identify differentially expressed gene products. Our goal is to identify a new set of genes induced or repressed during DC maturation elicited by rmTNF alpha treatment.

Multiplex messenger assay: simultaneous, quantitative measurement of expression of many genes in the context of T cell activation

The hybridization signature approach, using colony filters and labeled complex probes, can provide high throughput measurement of gene activity. We describe here the implementation of this method to follow the expression levels of 47 genes in resting and activated T cells, as well as in epithelial cells. Using 4-fold spotting of colonies, imaging plate detection and various correction and normalization procedures, the technique is sensitive enough to quantify expression levels for sequences present at 0.005% abundance in the probe. Comparison with Northern blotting shows good consistency between the two methods. Upon activation of a T cell clone by an anti-CD3 antibody variations ranging from 2- to 20-fold are measured, some of which had not been reported previously. This 'multiplex messenger assay' method, performed using available commercial apparatus, can be used in many cases where simultaneous assessment of mRNA levels for many genes is of interest.

From hybridization image to numerical values: a practical, high throughput quantification system for high density filter hybridizations

Hybridization to sets of bacterial colonies or PCR products arrayed on high density filters is used in a number of experimental schemes. In many cases it is desirable to collect quantitative information ('hybridization signatures') rather than indications on 'positive' and 'negative' colonies. We present a practical system, based on an imaging plate analyser and a customized version of commercial software, that makes such quantification feasible, and define its performance in terms of reproducibility and linearity. The system is far superior to methods based on autoradiography and should be useful in many projects that involve the increasingly popular high density filter format.

Differential gene expression in the murine thymus assayed by quantitative hybridization of arrayed cDNA clones

High-throughput measurement of hybridization signatures obtained using complex probes prepared from poly(A)+ RNA and high-density cDNA colony filters is described. The performance of the system, elimination of artifacts, and verification of the validity of the data are discussed. cDNAs corresponding to sequences present at levels of approximately 0.01% in the complex probe can be detected. Good correlation is observed between expression profiles determined by this method and by Northern blotting. The method is applied to a preliminary investigation of differential expression in three cell types present in the murine thymus.

Genome programmes: an opportunity for biology

The development of human molecular genetics in the eighties led to the implementation of projects aimed at a systematic study of the human genetic make-up--the so-called "Genome Projects". These have so far been mainly concerned with genome mapping, both by family studies using polymorphic markers (genetic mapping) and by direct analysis of DNA with suitable fractionation and cloning methods (physical mapping). Major progress has been made in both fields recently. Sequencing per se has remained limited because of technical constraints, although systematic cDNA sequencing has caught on in a large way. National policies are quite diverse, with the USA, the UK, France and Japan being the major players; funding sources range from governments to foundations. Many of the results, methods and concepts obtained or implemented during genome studies can be of great use to "conventional" laboratories, and efficient interfacing between these two worlds is an increasingly important issue.

Cloning and sequence analysis of a flo/lfy homologue isolated from cauliflower (Brassica oleracea L. var. botrytis)

A cDNA library has been constructed from cauliflower curd in which floral development had been initiated. Two cDNAs (pBOFH3 and pBOFH8) have been isolated using the Antirrhinum flo gene as a heterologous probe. The two clones were sequenced and found to contain introns. Comparison of the deduced cDNA sequence of bofh with flo and the Arabidopsis homologue lfy reveals extensive homology. An mRNA transcript of 1.6 kb appears on northern RNA blots. This transcript can be detected, at low levels, before any obvious signs of floral differentiation, reflecting the role bofh plays in determining floral meristem identity.

Laser microdissection of the fragile X region: identification of cosmid clones and of conserved sequences in this region

Laser microdissection has been used to dissect material from the X-chromosome region involved in fragile-X-linked mental retardation. After dissection, single chromosome slices corresponding to this fragile site were subjected to DNA amplification using either a vector ligation method (to provide known anchor sequences) or primer oligonucleotides corresponding to the ubiquitous Alu sequences. Amplified material was then cloned or, alternately, used to screen a gridded cosmid library. Eight cosmid clones identified in this way were regionally mapped using a panel of hybrid cell lines and shown to originate from a narrow interval centered on the fragile X site. Two clones are included in the approximately 6-cM interval defined by probes RNI (DXS369, 5 cM proximal) and VK21 (DXS 296, 1-2 cM distal) and which includes the fragile site, and at least one clone contains sequences conserved across species suggestive of a gene. This method combines the focused approach of microdissection and the convenience of obtaining cosmid (rather than small-insert) clones; it may be useful for studies of other defined chromosomal regions.

Changes to the Stoichiometry of Glycine Decarboxylase Subunits during Wheat (Triticum aestivum L.) and Pea (Pisum sativum L.) Leaf Development

Changes in the levels of the four subunits of the mitochondrial enzyme glycine decarboxylase (EC 2.1.2.10) have been investigated during development in the 8 day old primary leaf of wheat (Triticum aestivum L.). Proteins were extracted from wheat leaf sections between the basal meristem and 8.5 centimeters. The individual glycine decarboxylase subunits were detected by Western blotting, using subunit-specific polyclonal antibodies, and quantified by laser densitometry. P, T, and H subunits showed similar developmental patterns along the leaf. All were below the level of detection up to 1.5 centimeters from the meristem, but then increased over the leaf length examined. In contrast, the increase in the L protein (lipoamide dehydrogenase) was more gradual, and levels in the youngest regions of the leaf were maintained at approximately 14% of those at 8.5 centimeters. In a complementary study, levels of the four subunits in light-grown leaf tissues were compared to those in etiolated leaves from wheat and pea (Pisum sativum L.), using the activity of the mitochondrial marker enzyme fumarase as the basis for comparison. For both wheat and pea, levels of P, T, and H proteins in etiolated tissues were between 25 and 30% of those in lightgrown tissue. However, in etiolated tissues L protein was present at levels of 60 to 70% of that in light-grown tissues. The results indicate that discrete mechanisms may control the synthesis of L, as compared to P, T, and H proteins.

Reduction in cab and psb A RNA transcripts in response to supplementary ultraviolet-B radiation

The cab and psb A RNA transcript levels have been determined in Pisum sativum leaves exposed to supplementary ultraviolet-B radiation. The nuclear-encoded cab transcripts are reduced to low levels after only 4 h of UV-B treatment and are undetectable after 3 days exposure. In contrast, the chloroplast-encoded psb A transcript levels, although reduced, are present for at least 3 days. After short periods of UV-B exposure (4 h or 8 h), followed by recovery under control conditions, cab RNA transcript levels had not recovered after 1 day, but were re-established to ca. 60% of control levels after 2 more days. Increased irradiance during exposure to UV-B reduced the effect upon cab transcripts, although the decrease was still substantial. These results indicate rapid changes in the cellular regulation of gene expression in response to supplementary UV-B and suggest increased UV-B radiation may have profound consequences for future productivity of sensitive crop species.

Fragile X-linked mental retardation and the difficulties of reverse genetics

Fragile X-linked mental retardation is an enigmatic inheritable syndrome in which severe mental retardation, a cytogenetically detectable fragile site at Xq27.3 (FraX) and a number of dysmorphic features are associated. Genetic analysis shows that the mode of inheritance is more complex than a straightforward X-linked recessive trait and probably involves a two-step process for which several models have been proposed. Early attempts at 'cloning the fragile site' provided several DNA segments lying in its general vicinity, and large scale DNA mapping methods were extensively applied in an effort to generate maps including this region. These efforts were complemented by more focussed methods such as microdissection; together these approaches have now provided a number of DNA segments within a 5 cM interval around FraX, and with the help of these new probes the site is indeed being cloned. Unravelling the nature of the sequence(s) responsible for the mental retardation syndrome will probably take some time, however.

Very high molecular weight DNA for pulsed field gel studies can be obtained routinely from conventional frozen blood aliquots

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A simple method for the direct use of total cosmid clones as hybridization probes

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The gene encoding L1, a neural adhesion molecule of the immunoglobulin family, is located on the X chromosome in mouse and man

The murine and human genes for the L1 neural adhesion molecule were shown to lie on conserved regions of the X chromosome to which genes responsible for several neuromuscular diseases have been mapped and which are adjacent to the fragile site (FRAXA) associated with mental retardation. By pulsed-field gel mapping we have demonstrated physical linkage between the L1 gene and other genes located in Xq28: L1 lies between the eye pigment RCP, GCP locus and the glucose-6-phosphate dehydrogenase (G6PD) gene. This location is compatible with the implication of the L1 molecule in one of the X-linked neuromuscular diseases mapped to this region.

Delineation of determinants on HLA-B7 and HLA-B27 that are necessary for cytolytic T cell recognition by using inter- and intra-domain recombinants

We have used bulk culture HLA-B7 and HLA-B27 specific CTL lines derived from 11 donors, and a series of rHLA-B7/HLA-B27 genes transfected into and expressed on the surface of the murine cell P815, to determine the amino acid residues on these HLA class I molecules that are critical for allospecific CTL recognition. The results obtained indicate that for four of six HLA-B7-specific CTL lines the alpha-1 domain for CTL recognition. Furthermore, we found that residues 77 and/or 80 had a critical effect on recognition for all of the CTL lines tested. The region 97-156 in the alpha-2 domain was also important for some of these CTL lines. Furthermore, by using five bulk culture HLA-B27-specific CTL lines we were able to show that residues 77 and/or 80 and residue 152 are also essential for recognition of HLA-B27 by HLA-B27-specific CTL. The strong influence exerted by these residues is discussed in terms of the three-dimensional structure of class I molecules. Finally, a selection was regularly observed in the bulk cultures such that the CTL that were preferentially influenced by either the alpha-1 or the alpha-2 domain were lost after 4 to 7 wk of culture resulting in CTL cell lines which were extremely sensitive to sequence modifications of HLA-B7 or HLA-B27. The possible reasons for this selection, which we have previously observed with both anti-HLA-A2 and anti-HLA-A3 cell lines and is therefore not unique to HLA-B7 or HLA-B27, are discussed.

Delineation of determinants on HLA-B7 and HLA-B27 that are necessary for cytolytic T cell recognition by using inter- and intra-domain recombinants

We have used bulk culture HLA-B7 and HLA-B27 specific CTL lines derived from 11 donors, and a series of rHLA-B7/HLA-B27 genes transfected into and expressed on the surface of the murine cell P815, to determine the amino acid residues on these HLA class I molecules that are critical for allospecific CTL recognition. The results obtained indicate that for four of six HLA-B7-specific CTL lines the alpha-1 domain for CTL recognition. Furthermore, we found that residues 77 and/or 80 had a critical effect on recognition for all of the CTL lines tested. The region 97-156 in the alpha-2 domain was also important for some of these CTL lines. Furthermore, by using five bulk culture HLA-B27-specific CTL lines we were able to show that residues 77 and/or 80 and residue 152 are also essential for recognition of HLA-B27 by HLA-B27-specific CTL. The strong influence exerted by these residues is discussed in terms of the three-dimensional structure of class I molecules. Finally, a selection was regularly observed in the bulk cultures such that the CTL that were preferentially influenced by either the alpha-1 or the alpha-2 domain were lost after 4 to 7 wk of culture resulting in CTL cell lines which were extremely sensitive to sequence modifications of HLA-B7 or HLA-B27. The possible reasons for this selection, which we have previously observed with both anti-HLA-A2 and anti-HLA-A3 cell lines and is therefore not unique to HLA-B7 or HLA-B27, are discussed.

In situ hybridization and pulsed-field gel analysis define two major minisatellite loci: 1q23 for minisatellite 33.6 and 7q35-q36 for minisatellite 33.15

The two classical minisatellite probes, 33.6 and 33.15, were used for in situ hybridization to human metaphase chromosomes. Surprisingly, a single major hybridization peak was observed with each probe, respectively at 1q23 for 33.6 and 7q35-q36 for 33.15. Hybridization to human DNA cleaved with "rare-cutter" enzymes and fractionated on pulsed-field gels also showed a fairly simple, largely monomorphic pattern which allows chromosomal assignment using somatic cell hybrids. Differences in hybridization stringency and degree of resolution account for most of the discrepancy between these results and the accepted view of minisatellites, i.e., a large number of unlinked loci spread over the genome. Our results nevertheless indicate the existence of particularly large and homologous loci on a particular chromosome for each of these probes.