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.

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.

Mitochondrial DNA variation of Triatoma infestans populations and its implication on the specific status of T. melanosoma

DNA sequence comparison of 412 base-pairs fragments of the mitochondrial cytochrome B gene was used to infer the genetic structure of nine geographical Triatoma infestans populations and their phylogenetic relationship with T. melanosoma and T. brasiliensis. T. infestans and T. melanosoma were compared by morphometry, allozyme and cytogenetic analyses, as well as subjected to reciprocal crosses, in order to clarify the taxonomic status of the latter. No differences were found to distinguish the two species and the crosses between them yielded progeny. T. infestans populations presented four haplotypes that could be separated in two clusters: one formed by the samples from Bolivia (Andes and Chaco) and the other formed by samples from Argentina and Brazil. Silvatic and domestic T. infestans populations from Bolivia (Andes) were genetically identical.

Effect of arsenic on regulatory T cells

INTRODUCTION

Arsenic (As) affects the function and survival of lymphocytes, and some arsenic compounds exert a relevant antineoplastic effect. We have explored the effect of As on T regulatory cells.

RESULTS AND DISCUSSION

In vitro experiments with peripheral blood mononuclear cells from healthy subjects showed that low concentrations of As tended to increase the number of natural T regulatory (nTreg) lymphocytes, whereas concentrations >5.0 muM had an opposite effect. Furthermore, rats exposed to As showed redistribution of nTreg cells, and As administration to rats with experimental allergic encephalomyelitis increased the levels of nTreg cells in spleen and diminished the severity of this condition. On the other hand, in 47 apparently healthy subjects chronically exposed to As, we found significant inverse correlation between urinary As levels and the number and function of nTreg lymphocytes. Although most of these individuals showed enhanced levels of apoptotic lymphocytes in peripheral blood, with a diminution of mitochondrial membrane potential, no significant correlation between these parameters and urinary As was detected.

CONCLUSION

Our data indicate that As seems to have a relevant and complex effect on nTreg cells.

Differential gene expression in CD3epsilon- and RAG1-deficient thymuses: definition of a set of genes potentially involved in thymocyte maturation

A set of 3000 mouse thymus cDNAs was analyzed by extensive measurement of expression using complex-probe hybridization of DNA arrays ("quantitative differential screening"). The complex probes were initially prepared using total thymus RNA isolated from C57BL/6 wild-type (WT), CD3epsilon- and RAG1-deficient mice. Over 100 clones displaying over- or under-expression by at least a factor of two between WT and knockout (KO) thymuses were further analyzed by measuring hybridization signatures with probes from a wide range of KO thymuses, cell types, organs, and embryonic thymuses. A restricted set of clones was selected by virtue of their expression spectra (modulation in KO thymuses and thymocytes, lymphoid cell specificity, and differential expression during embryonic thymus development), sequenced at one extremity, and compared to sequences in databases. Clones corresponding to previously identified genes (e.g., Tcrbeta, Tcf1 or CD25) showed expression patterns that were consistent with existing data. Ten distinct clones corresponding to new genes were subjected to further study: Northern blot hybridization, in situ hybridization on thymus sections, and partial or complete mRNA sequence determination. Among these genes, we report a new serine peptidase highly expressed in cortical epithelial cells that we have named thymus-specific serine peptidase (TSSP), and an acidic protein expressed in thymocytes and of unknown function that we have named thymus-expressed acidic protein (TEAP). This approach identifies new molecules likely to be involved in thymocyte differentiation and function.

T-cell lymphoma revealed by a peripheral neuropathy. A report of two cases with an immunohistologic study on lymph node and nerve biopsies

In two patients a peripheral neuropathy was the presenting symptom of a noncutaneous peripheral T-cell lymphoma. In the first patient, the neuropathy had a relapsing and remitting course, the symptoms improved under corticosteroid therapy. The second patient suffered from a relentless neuropathy. In both cases the lymphoma infiltrated the peroneal nerve with an angiocentric and perivascular pattern resembling that observed in central nervous system lymphomas. The characterization of T-cell subsets in the lymph node showed cells with the helper/inducer and suppressor/cytotoxic phenotype in the first case and a predominance of cells with the helper/inducer phenotype in the second case. In the nerve, lymphocytes beard the helper/inducer phenotype antigen. A typical paraneoplastic vasculitis of nerve showed clearly different immunologic features.

Acute mesenteric ischaemia: a pictorial review

Abstract

Acute mesenteric ischaemia (AMI) is an uncommon cause of acute hospital admission with high mortality rates (50–90%) that requires early diagnosis and treatment. With the increase in average life expectancy, AMI represents one of the most threatening abdominal conditions in elderly patients. Untreated, AMI will cause mesenteric infarction, intestinal necrosis, an overwhelming inflammatory response and death. Early intervention can reverse this process leading to a full recovery, but the diagnosis of AMI is difficult. The failure to recognise AMI before intestinal necrosis has developed is responsible for the high mortality of the disease. Unfortunately, common CT findings in bowel ischaemia are not specific. Therefore, it is often a combination of nonspecific clinical, laboratory and radiological findings that helps most in the correct interpretation of CT findings. The purpose of this article is to provide an overview of the anatomy, physiology of mesenteric perfusion and discussions of causes, pathogenesis and CT findings in various types of acute bowel ischaemia. Familiarity with various imaging features of mesenteric injury is essential to make a timely diagnosis that will lead to improved patient outcomes.

Teaching Points

• AMI is a potentially life-threatening disorder whose prognosis depends on early recognition, accurate diagnosis and timely intervention.

• Arterial inflow occlusion due to thrombosis or embolisation is the most common cause of AMI.

• Four aetiological types of AMI have been associated with different characteristics and risk factors (EAMI, TAMI, VAMI and NOMI).

• Physical examination and laboratory findings are not sensitive or specific for diagnosing AMI; therefore, MDCT is still the first-line imaging method in suspected AMI.

• Although a number of scoring systems for prognosis have been proposed, these have not been validated in large-scale studies.

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.

The effect of RU486 on the gene expression profile in an endometrial explant model

Administration of RU486 in vivo during the receptive phase rapidly renders the endometrium non-receptive to the implanting embryo. In order to identify key pathways responsible for endometrial receptivity we have used cDNA arrays to monitor gene expression changes in short-term endometrial explants in response to RU486. Endometrial biopsies from five normal fertile women at mid-secretory phase were cultured in the presence of estradiol and progesterone with or without RU486 for 12 h. cDNA arrays were produced containing approximately 1000 sequence-verified clones which included genes known to be important in angiogenesis, apoptosis, cell signalling, extracellular matrix remodelling and cell cycle regulation. cDNA probes from the paired endometrial samples were hybridized to the arrays and hybridization signals were quantified. A total of 12 genes displayed significant changes in expression; six were up-regulated and six down-regulated following RU486 treatment. For five of these genes this is the first report suggesting that they are regulated by steroids in the endometrium. JAK1 and JNK1 were two of the genes shown by the arrays to be down-regulated in RU486-treated endometrial explants. This was confirmed by real time RT-PCR. JAK1 immunoreactivity was localized to both glandular epithelium and the stroma of normal endometrium and staining was much stronger in the luteal phase of the cycle. These results show that components of two important signalling pathways in endometrium-the JAK/STAT pathway, and the JNK pathway-are altered by RU486. Genes whose expression is controlled by these pathways are likely to be involved in the mechanism by which steroids render the endometrium receptive to the implanting embryo.

Replication of the tumor necrosis factor receptor-associated factor 1/complement component 5 region as a susceptibility locus for rheumatoid arthritis in a European family-based study

OBJECTIVE

We recently showed, using a candidate gene approach in a case-control association study, that a 65-kb block encompassing tumor necrosis factor receptor-associated factor 1 (TRAF1) and C5 is strongly associated with rheumatoid arthritis (RA). Compared with case-control association studies, family-based studies have the added advantage of controlling potential differences in population structure and are not likely to be hampered by variation in population allele frequencies, as is seen for many genetic polymorphisms, including the TRAF1/C5 locus. The aim of this study was to confirm this association in populations of European origin by using a family-based approach.

METHODS

A total of 1,356 western European white individuals from 452 "trio" families were genotyped for the rs10818488 polymorphism, using the TaqMan allelic discrimination assay.

RESULTS

We observed evidence for association, demonstrating departure from Mendel's law, with an overtransmission of the rs10818488 A allele (A = 55%; P = 0.036). By taking into consideration parental phenotypes, we also observed an increased A allele frequency in affected versus unaffected parents (A = 64%; combined P = 0.015). Individuals carrying the A allele had a 1.2-fold increased risk of developing RA (allelic odds ratio 1.24, 95% confidence interval 1.04-1.50).

CONCLUSION

Using a family-based study that is robust against population stratification, we provide evidence for the association of the TRAF1/C5 rs10818488 A allele and RA in populations of European descent, further substantiating our previous findings. Future functional studies should yield insight into the biologic relevance of this locus to the pathways involved in RA.

Identification of the putative ancestral allele of bovine single-nucleotide polymorphisms

Identifying the action of natural selection from patterns of standing genetic variation has long been of interest to the population genetic community. Thanks to the availability of large single-nucleotide polymorphism (SNP) data sets for many species and of high-throughput SNP genotyping methods, whole-genomic surveys to detect selective sweeps are now possible. Knowing the ancestral allele increases the power to detect selection. We present here a comparative genomic approach to determine the putative ancestral allele of bovine SNPs deposited in public databases. We analysed 19,551,488 SNPs and identified the putative ancestral allele for 14,339,107 SNPs. Our predicted ancestral alleles were in agreement with ancestral alleles detected by genotyping outgroup species for 97% SNPs from the BovineSNP50 BeadChip. This comparison indicates that our comparative genomic-based approach to identify putative ancestral alleles is reliable.

Detection of signatures of selective sweeps in the Blonde d'Aquitaine cattle breed

Identifying recent positive selection signatures in domesticated animals could provide information on genome response to strong directional selection from domestication and artificial selection and therefore could help in identifying mutations responsible for improved traits. We used genotyping data generated using Illumina's BovineSNP50 Genotyping BeadChips to identify selection signatures in the Blonde d'Aquitaine breed, a well-muscled French beef breed. For this purpose, we employed a hidden Markov model-based test, which detects selection by studying local variations in the allele frequency spectrum along the genome, within a single population. Three regions containing selective sweeps were identified. Annotation of genes located within these regions revealed interesting candidate genes. For example, myostatin (also known as GDF8), a known muscle growth factor inhibitor, is located within the selection signature region found on chromosome 2. In addition, we have identified chromosomal regions that show some evidence of selection within QTL regions for economically important traits. The results of this study could help to better understand the mechanisms related to the selection of the Blonde d'Aquitaine breed.

A major SNP resource for dissection of phenotypic and genetic variation in Pacific white shrimp (Litopenaeus vannamei)

Bioinformatics and re-sequencing approaches were used for the discovery of sequence polymorphisms in Litopenaeus vannamei. A total of 1221 putative single nucleotide polymorphisms (SNPs) were identified in a pool of individuals from various commercial populations. A set of 211 SNPs were selected for further molecular validation and 88% showed variation in 637 samples representing three commercial breeding lines. An association analysis was performed between these markers and several traits of economic importance for shrimp producers including resistance to three major viral diseases. A small number of SNPs showed associations with test weekly gain, grow-out survival and resistance to Taura Syndrome Virus. Very low levels of linkage disequilibrium were revealed between most SNP pairs, with only 11% of SNPs showing an r(2)-value above 0.10 with at least one other SNP. Comparison of allele frequencies showed small changes over three generations of the breeding programme in one of the commercial breeding populations. This unique SNP resource has the potential to catalyse future studies of genetic dissection of complex traits, tracing relationships in breeding programmes, and monitoring genetic diversity in commercial and wild populations of L. vannamei.

Exposure to constant light during testis development increases daily sperm production in adult Wistar rats

Testis histometry and daily sperm production (DSP) were evaluated in adult (160-day-old) Wistar rats exposed to constant light for the first 25 days after birth, and compared with control animals which were exposed to a 12 h-light-12 h-dark light regimen. Significantly greater (P < 0.05) numbers of Sertoli cell nucleoli and round spermatids per cross-section of seminiferous tubule were found in animals exposed to constant light. In addition, epididymis weight, DSP per testis and per gram of testis, as well as Leydig cell compartment volume, were significantly increased in treated animals. Although there was a clear trend toward an increased Sertoli cell population per testis in animals exposed to constant light, this difference was not statistically significant (P < 0.05). The number of round spermatids as expressed per Sertoli cell was the same in both groups. Surprisingly, the diameter and volume of round spermatid nucleus at stages I and VII of the cycle of seminiferous epithelium were significantly lower (P < 0.05) in treated animals. In conclusion, constant illumination during neonatal testis development increased sperm production and Leydig cell compartment volume in adult rats probably through a mechanism involving elevated follicle stimulating hormone and luteinizing hormone during the prepubertal period. To our knowledge, this is the first study showing that altering the light regimen can affect sperm production in non-seasonal breeders.

Genome-wide linkage disequilibrium in the Blonde d'Aquitaine cattle breed

We present here the first genome-wide characterization of linkage disequilibrium (LD) in the French Blonde d'Aquitaine (BLA) breed, a well-muscled breed renowned for producing high-yielding beef carcasses. To assess the pattern and extent of LD, we used a sample of 30 unrelated bulls and 36 923 single nucleotide polymorphisms (SNPs) covering all cattle autosomes. The squared correlation of the alleles at two loci (r(2) ) was used as a measure of LD. The analysis of adjacent marker pairs revealed that the level of LD decreases rapidly with physical distance between SNPs. Overall mean r(2) was 0.205 (±0.262). Strong LD (r(2)  > 0.8) and useful LD (measured as r(2 ) > 0.2) were observed within genomic regions of up to 720 and 724 kb, respectively. We analysed the genetic structure of the BLA population and found stratification. The observed genetic sub-structuring is consistent with the known recent demographic history that occurred during BLA breed formation. Our results indicate that LD mapping of phenotypic traits in the BLA population is feasible; however, because of this sub-structuring, special care is needed to reduce the likelihood of false-positive associations between marker loci and traits of interest.

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.

Prospecting for pig single nucleotide polymorphisms in the human genome: have we struck gold?

Gene-to-gene variation in the frequency of single nucleotide polymorphisms (SNPs) has been observed in humans, mice, rats, primates and pigs, but a relationship across species in this variation has not been described. Here, the frequency of porcine coding SNPs (cSNPs) identified by in silico methods, and the frequency of murine cSNPs, were compared with the frequency of human cSNPs across homologous genes. From 150,000 porcine expressed sequence tag (EST) sequences, a total of 452 SNP-containing sequence clusters were found, totalling 1394 putative SNPs. All the clustered porcine EST annotations and SNP data have been made publicly available at http://sputnik.btk.fi/project?name=swine. Human and murine cSNPs were identified from dbSNP and were characterized as either validated or total number of cSNPs (validated plus non-validated) for comparison purposes. The correlation between in silico pig cSNP and validated human cSNP densities was found to be 0.77 (p < 0.00001) for a set of 25 homologous genes, while a correlation of 0.48 (p < 0.0005) was found for a primarily random sample of 50 homologous human and mouse genes. This is the first evidence of conserved gene-to-gene variability in cSNP frequency across species and indicates that site-directed screening of porcine genes that are homologous to cSNP-rich human genes may rapidly advance cSNP discovery in pigs.

Analysis of public single nucleotide polymorphisms in commercial pig populations

More than 5500 pig single nucleotide polymorphisms (SNPs) were recently identified and deposited in the public domain. To test the usefulness of these public SNPs, 109 SNPs were analysed for polymorphism within six commercial pig populations. A functional polymerase chain reaction (PCR) assay was obtained for 103 SNPs and it was possible to validate c. 59% by PCR-restriction fragment length polymorphism. Furthermore, polymorphism was found using a relatively limited number of genomic DNA samples, indicating that these polymorphisms are segregating at a useful frequency in these populations. The high percentage of validated markers demonstrates the utility of these public pig SNPs to identify loci responsible for economically important traits in commercial pig populations.

Cervical Artery Dissections with and without stroke, risk factors and prognosis: a Chilean prospective cohort

We aimed to characterize spontaneous cervical artery dissection (CeAD) patients with and without stroke and describe risk factors for cerebrovascular complications in a Chilean prospective cohort.

METHODS

Consecutive CeAD patients admitted to a Chilean center confirmed by neuroimaging. Logistic regression was used.

RESULTS

168 patients were included, median follow-up time was 157 days. Stroke occurred in 49 (29.2%) cases, 4 (2%) patients died, all of whom had a stroke, and 10 (6%) presented CeAD recurrence. In univariate analyses, men (odds ratio [OR] 3.97, 95% confidence interval [CI] 1.97-8.00, P < 0.001), internal carotid artery CeAD (OR 2.82, 95% CI 1.38-5.78, P = 0.005) and vessel occlusion (OR 4.45, 95% CI 1.38-14.38, P = 0.035) increased stroke risk. Conversely, vertebral artery dissection (OR 0.35, 95% CI 0.16-0.74, P = 0.006) and longer symptom onset to admission (O-A) time (OR 0.79, 95% CI 0.70-0.90, P < 0.001) were associated to decreased stroke risk. After multivariate analysis, men (OR 2.88, 95% CI 1.32-6.27, P = 0.008) and O-A time (OR 0.80, 95% CI 0.69-0.92, P = 0.002) remained independently associated with stroke.

CONCLUSION

CeAD presented commonly as a non-stroke entity, with favorable prognosis. Albeit to a higher frequency of CeAD in women, stroke occurred predominantly in men, who were admitted earlier.

Characterization of the porcine FSCN3 gene: cDNA cloning, genomic structure, mapping and polymorphisms

Fascin 3 (FSCN3)is a testis-specific actin-bundling protein involved in spermatid development. Here we describe the molecular characterisation of the porcine FSCN3 gene. The 1,800-bp cDNA sequence contains a 1,497-bp open reading frame encoding a protein of 498 amino acids with a calculated molecular mass of 56.2 kDa and an isoelectric point of 6.82. The porcine FSCN3 protein shares high identity with other mammalian FSCN3. The FSCN3 gene contains seven exons, spans approximately 9 kb, and maps to pig chromosome 18. We also identified 24 DNA polymorphisms.

Single nucleotide polymorphism identification, linkage and radiation hybrid mapping of the porcine pituitary adenylate cyclase-activating polypeptide type I receptor gene to chromosome 18

Pituitary adenylate cyclase-activating polypeptide (PACAP) is a neuropeptide with diverse biological actions. Type I PACAP receptors (PACAPR) are specific for PACAP, whereas type II and III PACAPRs are less restricted. To localize and analyse the variation of this gene, a 559-bp long intronic fragment of the porcine PACAPR gene was amplified by polymerase chain reaction and sequenced in samples from five different pig breeds. One single nucleotide polymorphism was identified and its allele frequency was determined in all five breeds. Linkage analysis in a Berkshire x Yorkshire reference family placed the PACAPR gene on chromosome 18, between SW787 and S0062 (SW787- 8.1 cM -PACAPR- 3.0 cM -S0062). Radiation hybrid mapping confirmed that the PACAPR gene was linked to SW1682 on chromosome 18 (28.8 cR(3000); LOD = 10.4).

Detection of selection signatures in Limousin cattle using whole-genome resequencing

Limousin, a renowned beef breed originating from central France, has been selectively bred over the last 100 years to improve economically important traits. We used whole-genome sequencing data from 10 unrelated Limousin bull calves to detect polymorphisms and identify regions under selection. A total of 13 943 766 variants were identified. Moreover, 311 852 bi-allelic SNPs and 92 229 indels located on autosomes were fixed for the alternative allele in all sequenced animals, including the previously reported missense deleterious F94L mutation in MSTN. We performed a whole-genome screen to discover genomic regions with excess homozygosity, using the pooled heterozygosity score and identified 171 different candidate selective sweeps. In total, 68 candidate genes were found in only 57 of these regions, indicating that a large fraction of the genome under selection might lie in non-coding regions and suggesting that a majority of adaptive mutations might be regulatory in nature. Many QTL were found within candidate selective sweep regions, including QTL associated with shear force or carcass weight. Among the putative selective sweeps, we located genes (MSTN, NCKAP5, RUNX2) that potentially contribute to important phenotypes in Limousin. Several candidate regions and genes under selection were also found in previous genome-wide selection scans performed in Limousin. In addition, we were able to pinpoint candidate causative regulatory polymorphisms in GRIK3 and RUNX2 that might have been under selection. Our results will contribute to improved understanding of the mechanisms and targets of artificial selection and will facilitate the interpretation of GWASs performed in Limousin.