Polymorphisms in the large subunit of human RNA polymerase II as target for allele-specific inhibition.

The lack of specificity of cancer treatment causes damage to normal cells as well, which limits the therapeutic range. To circumvent this problem one would need to use an absolute difference between normal cells and cancer cells as therapeutic target. Such a difference exists in the genome of all individuals suffering from a tumor that is characterized by loss of genetic material [loss of heterozygosity (LOH)]. Due to LOH, the tumor is hemizygous for a number of genes, whereas the normal cells of the individual are heterozygous for these genes. Theoretically, polymorphic sites in these genes can be utilized to selectively target the cancer cells with an antisense oligonucleotide, provided that it can discriminate the alleles and inhibit gene expression. Furthermore, the targeted gene should be essential for cell survival, and 50% gene expression sufficient for the cell to survive. This will allow selective killing of cancer cells without concomitant toxicity to normal cells. As an initial step in the experimental test of this putative selective cancer cell therapy, we have developed a set of antisense phosphorothioate oligonucleotides which can discriminate the two alleles of a polymorphic site in the gene encoding the large subunit of RNA polymerase II. Our data show that the exact position of the antisense oligonucleotide on the mRNA is of essential importance for the oligo-nucleotide to be an effective inhibitor of gene expression. Shifting the oligonucleotide position only a few bases along the mRNA sequence will completely abolish the inhibitory activity of the antisense oligonucleotide. Reducing the length of the oligonucleotides to 16 bases increases the allele specificity. This study shows that it is possible to design oligonucleotides that selectively target the matched allele, whereas the expression level of the mismatched allele, that differs by one nucleotide, is only slightly affected.

Non-P-glycoprotein mediated mechanism for multidrug resistance precedes P-glycoprotein expression during in vitro selection for doxorubicin resistance in a human lung cancer cell line.

Two different mechanisms that contribute to multidrug resistance (MDR) were found in derivatives of the human squamous lung cancer cell line SW-1573. The parental cell line has a low amount of mdr1 P-glycoprotein mRNA. In three independent selections for doxorubicin resistance, MDR variants arose in which mdr1 P-glycoprotein mRNA and protein was not detectable. Selection on higher doxorubicin concentrations gave rise to variants containing high levels of mdr1 mRNA, due to transcriptional activation of the mdr1 gene. Upon continued selection for higher levels of doxorubicin resistance, the mdr1 gene became amplified, resulting in an additional increase in the level of mdr1 mRNA. The cross-resistance pattern of the sublines that lack mdr1 P-glycoprotein expression is different from that seen in the mdr1 overexpressing cells. Both types of MDR cell lines are resistant to doxorubicin, daunorubicin, etoposide, colchicine, gramicidin D, and vincristine. However, in the non-P-glycoprotein-mediated MDR cell lines, resistance levels are lower and a preferential resistance for etoposide is seen.

Identification of a functional initiator sequence in the human MDR1 promoter.

The sequence requirements for proper transcriptional initiation of the downstream human multidrug resistance MDR1 (P1) promoter were determined using a transient expression system in HeLa cells. The MDR1 promoter has no TATA box and the transcription start site has a strong homology with the initiator (Inr) sequence identified in the murine terminal deoxynucleotidyltransferase (TdT) gene. A deletion analysis showed that sequences from -6 to +11 relative to the P1 transcription start site were sufficient for proper transcriptional initiation, whereas deletion of sequences downstream of +11 resulted in a strong reduction of properly initiated transcripts. In this transient assay system, both the MDR1 and TdT initiator require in Hela cells the presence of an upstream activating sequence such as the SV40 enhancer. This is in contrast to the transcription in in vitro systems, in which the initiator sequence is able to direct transcription in the absence of an enhancer. Analysis of mutations in the initiator sequence from -8 to +10 showed that the A and T nucleotides at position +1 and +3, respectively, were essential, whereas other substitutions in this region had little effect on promoter activity.

The P-glycoprotein gene family of Caenorhabditis elegans. Cloning and characterization of genomic and complementary DNA sequences.

P-glycoproteins, encoded by families of evolutionarily conserved genes, can confer a multidrug-resistant phenotype to mammalian tumor cells. To obtain more information on their functions in normal cells we have cloned genomic and complementary DNA sequences of four P-glycoprotein gene homologs of the genetically well-characterized nematode Caenorhabditis elegans, termed pgp-1, pgp-2, pgp-3 and pgp-4, respectively. The genes were physically mapped on chromosome IV (pgp-1), I (pgp-2) and X (pgp-3 and pgp-4). Phenotypic mutants corresponding to these loci have not yet been described. Two of the genes, pgp-1 and pgp-3, were analyzed in detail. They are predicted to encode ATP-binding membrane-spanning proteins of 1321 and 1254 amino acid residues, respectively, with the characteristic features shared by most P-glycoproteins described thus far. Intra-species divergence of P-glycoprotein genes is more pronounced in C. elegans than in mammals. Only 40% of the amino acids of pgp-1 and pgp-3 are identical, in contrast to 77% identity between human MDR1 and MDR3. pgp-1 consists of 14 exons, pgp-3 of 13. The two genes share only one intron position, whereas they share four (pgp-1) and five (pgp-3) intron positions with mammalian P-glycoprotein genes. pgp-1, pgp-2, and pgp-3 are transcribed into low abundance mRNAs in wild-type nematodes. pgp-1 and pgp-3 mRNAs have the trans-spliced leader SL1 at their 5' ends. Arsenite, emetine and actinomycin D drugs did not increase the steady state levels of pgp mRNA, unlike in some mammalian cell types. Heat shock disturbed trans as well as cis-splicing of pgp-1 and led to the accumulation of partially processed pgp-1 RNA. Thus, in C. elegans these genes are not induced in the context of a general stress response, as has been proposed for mammalian P-glycoprotein genes in certain tissues.

Genes differentially expressed in medulloblastoma and fetal brain.

Serial analysis of gene expression (SAGE) was used to identify genes that might be involved in the development or growth of medulloblastoma, a childhood brain tumor. Sequence tags from medulloblastoma (10229) and fetal brain (10692) were determined. The distributions of sequence tags in each population were compared, and for each sequence tag, pairwise chi2 test statistics were calculated. Northern blot was used to confirm some of the results obtained by SAGE. For 16 tags, the chi2 test statistic was associated with a P value < 10(-4). Among those transcripts with a higher expression in medulloblastoma were the genes for ZIC1 protein and the OTX2 gene, both of which are expressed in the cerebellar germinal layers. The high expression of these two genes strongly supports the hypothesis that medulloblastoma arises from the germinal layer of the cerebellum. This analysis shows that SAGE can be used as a rapid differential screening procedure.

Effects of maternal thyroid status on thyroid hormones and growth in congenitally hypothyroid goat fetuses during the second half of gestation.

Congenital hypothyroidism in Dutch goats is due to a thyroglobulin (TG) synthesis defect that is inherited in an autosomal recessive manner. Minute amounts of mutated TG messenger RNA are translated into glycosylated TG fragments that contain the N-terminal hormonogenic site and are able to form T4, albeit less efficiently. We analyzed the effects of maternal thyroid status on fetal plasma thyroid hormones and growth during the second half of gestation (E90-E150). Maternal hypothyroidism, present from midgestation, resulted in decreased brain and cerebellum weights of affected goitrous fetuses, most evident at term gestation (E150). Brain and cerebellum weights of affected fetuses from unaffected mothers were not decreased. T4 and FT4 levels in affected fetuses were dependent on the maternal phenotype, as was the degree of enlargement of the goiter at E150. Newborn unaffected lambs from affected mothers had plasma T4 levels within the normal range. The present data show that in late gestation, fetal goats have to rely on their own thyroidal T4 production. The results suggest that affected fetuses are able to maintain sufficiently high T4 and T3 levels to prevent severe adverse effects of thyroid hormone deficiency on the brain if maternal iodide supply is adequate, although a possible increased transfer of maternal T4 to affected fetuses cannot be excluded. Under normal conditions, sufficient amounts of iodine are provided by the efficient iodine metabolism in euthyroid mothers. In affected mothers, much iodine is wasted because the thyroid also iodinates proteins other than the aberrant TG, resulting in insufficient iodine provision of the fetus and, consequently, in severe hypothyroidism.

An integrated map of chromosome 18 CAG trinucleotide repeat loci.

Expansions of trinucleotide CAG repeats have been demonstrated in at least eight neurodegenerative disorders, and suggested to occur in several others, including bipolar disorder and schizophrenia. Chromosome 18 loci have been implicated in bipolar disorder pedigrees by linkage analysis. To address this putative link between chromosome 18 CAG trinucleotide repeats and neuropsychiatric illness, we have screened a chromosome 18 cosmid library (LL18NCO2" AD") and identified 14 novel candidate loci. Characterisation of these loci involved repeat flank sequencing, estimation of polymorphism frequency and mapping using FISH as well as radiation hybrid panels. These mapped trinucleotide loci will be useful in the investigation of chromosome 18 in neurodegenerative or psychiatric conditions, and will serve to integrate physical and radiation hybrid maps of chromosome 18.

Effect of thyroid hormone deficiency on RC3/neurogranin mRNA expression in the prenatal and adult caprine brain.

Thyroid hormone deficiency has profound effects on the brain during development and less marked effects on the adult brain. These effects are considered to be the result of the direct regulation of specific target genes by thyroid hormone. Previous studies have shown that the expression of the neuronal gene RC3, encoding a 78-amino-acid calmodulin-binding protein kinase C substrate, is under the influence of thyroid hormone in vivo. In congenitally hypothyroid foetal goat at term (approximately 150 days of gestation), RC3 mRNA expression was reversibly decreased in the striatum but not in other brain regions. In the present study we investigated the role of thyroid hormone in RC3 mRNA expression at earlier stages of fetal development and in mature goats using in situ hybridization. There was a consistent decrease (35-80%) in the signal for RC3 mRNA per neuron in the striatum of hypothyroid adult and fetal goats of 90, 120 and 150 days of gestation compared to normal goats of the same age. In contrast, no consistent difference was observed in the cerebral cortex at any age studied. These data indicate that in both fetal and adult goats thyroid hormone, at least partly, affects the expression of RC3 mRNA in the striatum and not the cerebral cortex.

RC3/neurogranin structure and expression in the caprine brain in relation to congenital hypothyroidism.

In view of the profound effects of thyroid hormone deficiency on the central nervous system (CNS), neuronal genes regulated by thyroid hormone could potentially be involved in the development of the CNS. Expression of the neuronal gene RC3/neurogranin was shown to be induced by thyroid hormone in the rat. No data are available on RC3 expression in mammals with prenatal brain development, like humans. To study RC3 mRNA expression in a genetic in vivo model of congenital hypothyroidism, which also resembles the human situation in the timing of brain development relative to birth, we used an inbred strain of congenitally hypothyroid goats. We isolated a cDNA for the caprine RC3 homolog. The deduced amino acid sequence had 99% similarity with the rat and bovine protein sequence. An analysis of the developmental expression of RC3 mRNA levels showed a 3-fold increase between E90 and P0. In situ hybridization analysis showed that in euthyroid goats, the RC3 expression pattern was region-specific and resembled that in rats. However, in contrast to rats, hypothyroid goats showed only a reduced RC3 mRNA expression in the striatum. Hypothyroidism had no effect on RC3 mRNA expression in all other brain regions. T4-treatment of the hypothyroid fetus increased RC3 mRNA expression in the striatum to euthyroid control levels. These data suggest that thyroid hormone is a regulator of RC3 gene expression in the caprine brain, and that the striatum is highly sensitive to thyroid hormone deficiency.

Caprine homologue of rodent 5'-AMP-activated protein kinase subunit and yeast SNF4/CAT3 is down-regulated by thyroid hormone.

We isolated a cDNA, B12, that was down-regulated by thyroid hormone (TH) in the goat cerebellum, using a polymerase chain reaction (PCR)-based subtractive hybridization and differential screening procedure. Northern blot analysis of RNA from cerebellum of T4-treated and untreated hypothyroid goats confirmed that clone B12 was TH-regulated with an average reduction in expression of 21% after 4 days of T4 supplementation. Other tissues from a T4-treated and an untreated hypothyroid goat also revealed down-regulation of B12, with the highest reduction in expression found in the thyroid gland (38%). Steady-state levels of the approximately 1.8 kb B12 mRNA were higher in brain than in peripheral tissues. In situ hybridization showed that B12 mRNA in the brain is mainly present in various layers of the cerebellum and the cerebral cortex, the hippocampus, and the olfactory tubercle and is predominantly expressed in neurons. Sequence analysis of the caprine B12 cDNA clone, and the murine homologue, revealed 61% similarity to SNF4/CAT3, a regulator involved in the transcriptional control of glucose-repressible genes in yeast, and 99% identity to a rat 5'-AMP-activated protein kinase subunit, which is involved in the regulation of fatty acid, glycogen and isoprenoid metabolism. In view of these homologies, B12 might encode a regulator involved in distinct metabolic pathways and therefore, TH might also affect gene expression indirectly by down-regulation of regulators like B12.

Genetic transfer of non-P-glycoprotein-mediated multidrug resistance (MDR) in somatic cell fusion: dissection of a compound MDR phenotype.

A non-P-glycoprotein-mediated mechanism of multidrug resistance (non-Pgp MDR) has been identified in doxorubicin-selected sublines of the human non-small cell lung carcinoma cell line SW-1573. These sublines are cross-resistant to daunorubicin, VP16-213, Vinca alkaloids, colchicine, gramicidin D, and 4'-(9-acridinylamino)methanesulfon-m-anisidide (m-AMSA). They accumulate less drug than the parental cells and their resistance is not due to the MDR1-encoded P-glycoprotein, as the resistant cell lines have lost the low amount of MDR1 mRNA detectable in parental cells. Here we show that the resistant cell lines also contain less topoisomerase II mRNA and enzyme activity than the parental cells. This might contribute to the resistance of these lines to drugs interacting with topoisomerase II, such as doxorubicin, daunorubicin, and VP16-213, but cannot account for the resistance to the other drugs. We have tested whether all properties of the non-Pgp MDR cell lines cosegregate in somatic cell fusions between lethally gamma-irradiated, resistant donor cells and drug-sensitive acceptor cells. Whereas a MDR phenotype with reduced drug accumulation and the loss of MDR1 P-glycoprotein mRNA were cotransferred to the acceptor cells, the decrease in topoisomerase II gene expression was not. We conclude that the MDR phenotype, the reduced drug accumulation, and the loss of MDR1 P-glycoprotein mRNA are genetically linked. They might be due to a single dominant mutation, which does not cause the alteration in topoisomerase II.