Analysis of molecular intra-patient variation and delineation of a prognostic 12-gene signature in non-muscle invasive bladder cancer; technology transfer from microarrays to PCR.

BACKGROUND: Multiple clinical risk factors and genetic profiles have been demonstrated to predict progression of non-muscle invasive bladder cancer; however, no easily clinical applicable gene signature has been developed to predict disease progression independent of disease stage and grade. METHODS: We measured the intra-patient variation of an 88-gene progression signature using 39 metachronous tumours from 17 patients. For delineation of the optimal quantitative reverse transcriptase PCR panel of markers, we used 115 tumour samples from patients in Denmark, Sweden, UK and Spain. RESULTS: Analysis of intra-patient variation of the molecular markers showed 71% similar classification results. A final panel of 12 genes was selected, showing significant correlation with outcome. In multivariate Cox regression analysis, we found that the 12-gene signature was an independent prognostic factor (hazard ratio=7.4 (95% confidence interval: 3.4-15.9), P<0.001) when adjusting for stage, grade and treatment. Independent validation of the 12-gene panel and the determined cut-off values is needed and ongoing. CONCLUSION: Intra-patient marker variation in metachronous tumours is present. Therefore, to increase test sensitivity, it may be necessary to test several metachronous tumours from a patient's disease course. A PCR-based 12-gene signature significantly predicts disease progression in patients with non-muscle invasive bladder cancer.

A conserved human germline V kappa gene directly encodes rheumatoid factor light chains.

The full-length gene that encodes the light chain variable regions of an idiotypically related group of human IgM kappa rheumatoid factors (RFs) has been cloned and sequenced. The deduced amino acid sequence is identical to four separate RF proteins. These results prove that genes capable of encoding human anti-IgG autoantibody light chains without any somatic mutation are present in the kappa gene repertoire of normal people.

High level transcription of the glucocerebrosidase pseudogene in normal subjects and patients with Gaucher disease.

Gaucher disease is due to mutations involving the glucocerebrosidase gene. A closely homologous pseudogene is located approximately 16 kD downstream from the functional gene. Sequence analysis of clones from cDNA libraries made from skin fibroblast cultures showed several independent clones with the sequence of an aberrantly processed pseudogene message. Examination of cellular RNA from lymphoblasts or fibroblasts obtained from thirteen Gaucher disease patients, one Gaucher disease heterozygote, and four normal subjects showed that the pseudogene was consistently transcribed, and that in some cases the level of transcription seemed to be approximately equal to that of the functional gene. The transcription of the pseudogene must be taken into account when attempting to detect mutations of glucocerebrosidase by the study of cDNA libraries.

A glucocerebrosidase fusion gene in Gaucher disease. Implications for the molecular anatomy, pathogenesis, and diagnosis of this disorder.

The molecular diagnosis of Gaucher disease has been difficult due to the existence of several different point mutations in the glucocerebrosidase gene and due to the presence of a tightly linked, highly homologous pseudogene. We now report the occurrence of a "Lepore-like" glucocerebrosidase fusion gene in which the 5' end is the functional gene and the 3' end is the pseudogene. This further complicates the molecular diagnosis of Gaucher disease but sheds light on the molecular anatomy of the glucocerebrosidase gene complex and on the pathogenesis of this important storage disease.

An embryonic DNA-binding protein specific for the promoter of the retrovirus long terminal repeat.

Retrovirus expression is restricted in embryonal carcinoma (EC) cells but not in many differentiated cell lines. We used a very sensitive gel retardation assay to detect sequence-specific DNA-binding proteins in crude nuclear extracts obtained from EC and differentiated cells. Four binding sites were mapped in the noncoding sequences of the amphotropic murine leukemia virus. Strong binding to the CCAAT consensus sequence located in the promoter was specifically observed with EC nuclear extract. The binding protein is called EPBF (embryonal promoter-binding factor), and it is a candidate for the repressor of retrovirus transcription.

Amphotropic retrovirus vector system for human cell gene transfer.

Retroviral vectors have been constructed for gene transfer in mammalian and avian cells, however most retroviral vector systems are complicated by the spread of a replication-competent helper virus. This problem has been circumvented by segregating the viral genome into cis- and trans-acting components. By establishing helper cell lines that produce the trans-acting viral gene products, one can propagate the cis-acting component in them and harvest defective viral particles that contain only the cis-acting component. The cis-acting component can provide a useful vehicle for the highly efficient transfer of genes into target cells. The defective vector systems described to date, however, are restricted in host range to murine, avian, rat, and dog cells. We describe a helper-free vector system based entirely on an amphotropic murine virus with a wide mammalian host range, including the ability to carry out efficient gene transfer into human cells. We also describe a double mutation constructed in the trans-acting genome which reduces the frequency of replication-competent recombinant viruses to undetectable levels.

Mouse retroviral sequences acquired by cell lines after passaging through nude mice detected by hybridization of the fms probe pSM3.

The expression of a large RNA transcript, 8.5 to 9.5 kilobases, possibly related to the fms oncogene in mouse, rat, and human tumor cells, has been described in the literature. However, the pSM3 fms probe used to detect this gene transcript contains a significant amount of the pol gene of the Susan McDonough strain of feline sarcoma virus from which it was derived. Using a fms probe which does not contain any viral pol sequences, no such "fms-related" transcripts were detected in cell lines previously reported to express the large transcripts. These cell lines did express a large 9.5-kilobase transcript which hybridized to a probe for murine leukemia virus. Partial sequence analysis of the 9.5-kilobase transcript detected with the pSM3 probe in transformed rat cells indicated sequence homology with AKV murine leukemia virus. Thus, the presence of large RNA transcripts, interpreted by us and others as being related to the oncogene fms, appears to be due to the expression of mouse retroviral sequences which hybridize to the viral pol region contained in the pSM3 fms probe. In the case of rat and human cells, such sequences appear to be acquired after the cells have been passaged in nude mice. These results should serve as a reminder of the important biohazard and data interpretation implications for investigations in which cells transfected with retroviral vector constructs are injected into nude mice, because rescue of the recombinant sequences in these cells could occur following infection by endogenous murine retroviral particles.

Creating seamless junctions independent of restriction sites in PCR cloning.

A method is described for the efficient cloning of any given DNA sequence into any desired location without the limitation of naturally occurring restriction sites. The technique employs the polymerase chain reaction (PCR) combined with the capacity of the type-IIS restriction endonuclease (ENase) Eam1104I to cut outside its recognition sequence. Primers that contain the Eam1104I recognition site (5'-CTCTTC) are used to amplify the DNA fragments being manipulated. Because the ENase is inhibited by site-specific methylation in the recognition sequence, all internal Eam1104I sites present in the DNA can be protected by performing the PCR amplification in the presence of 5-methyldeoxycytosine (m5dCTP). The primer-encoded Eam1104I sites are not affected by the modified nucleotides (nt) since the newly synthesized strand does not contain any cytosine residues in the recognition sequence. In addition, the ENase's ability to cleave several bases downstream from its recognition site allows the removal of superfluous, terminal sequences from the amplified DNA fragments, resulting in 5' overhangs that are defined by the nt present within the cleavage site. Thus, the elimination of extraneous nt and the generation of unique, non-palindromic sticky ends permits the formation of seamless junctions in a directional fashion during the subsequent ligation event.

A bacteriophage lambda vector for the cloning and expression of immunoglobulin Fab fragments on the surface of filamentous phage.

We have combined the high cloning efficiency of the lambda bacteriophage vectors with the surface expression screening method for the display of combinatorial antibody fragment (Fab) libraries on the surface of filamentous phage particles. The utility of the herein described ImmunoZAP 13 system for the isolation of Fabs that specifically bind antigen is demonstrated using two phagemid display libraries prepared from a previously characterized human combinatorial library. The percentage of clones that specifically bind antigen is maintained throughout the process of subcloning the LC and VH genes into ImmunoZAP 13, in vivo mass excision to convert the lambda library to a phagemid library, and preparation of phagemid particles displaying Fabs. Specific phagemid were isolated from libraries containing 0.6% and 0.03% tetanus toxoid (TT)-binding clones after two and three rounds of biopanning, respectively. Relative binding curves determined on a small sample of isolated clones indicate that several unique immunoglobulin Fab fragments have been isolated.

Cloning in a bacteriophage lambda vector for the display of binding proteins on filamentous phage.

We have combined the efficiency and ease of use of bacteriophage lambda vectors with the power of phage display screening technology to create SurfZAP. The use of bacteriophage lambda allows the construction of large lambda expression libraries, which are rapidly and efficiently converted to stable plasmid libraries by mass excision. In SurfZAP, clones are expressed as fusions with amino acids 198-406 of the M13 minor coat protein (cpIII) and are displayed on the surface of filamentous phage. When produced with helper phage proteins, the fusion proteins are incorporated into the surface of phagemid particles. We demonstrate the utility of biopanning by isolating tetanus toxoid-binding mouse Fab clones from SurfZAP libraries. Approximately 10-100-fold enrichment of specific clones was observed after each panning round. The ability to create a large library of genotypes and screen the phenotypes by activity may be a potent methodology for basic research and drug discovery.

High-fidelity amplification using a thermostable DNA polymerase isolated from Pyrococcus furiosus.

A thermostable DNA polymerase which possesses an associated 3'-to-5' exonuclease (proofreading) activity has been isolated from the hyperthermophilic archaebacterium, Pyrococcus furiosus (Pfu). To test its fidelity, we have utilized a genetic assay that directly measures DNA polymerase fidelity in vitro during the polymerase chain reaction (PCR). Our results indicate that PCR performed with the DNA polymerase purified from P. furiosus yields amplification products containing less than 10% of the number of mutations obtained from similar amplifications performed with Taq DNA polymerase. The PCR fidelity assay is based on the amplification and cloning of lacI, lacO and lacZ alpha gene sequences (lacIOZ alpha) using either Pfu or Taq DNA polymerase. Certain mutations within the lacI gene inactivate the Lac repressor protein and permit the expression of beta Gal. When plated on a chromogenic substrate, these LacI- mutants exhibit a blue-plaque phenotype. These studies demonstrate that the error rate per nucleotide induced in the 182 known detectable sites of the lacI gene was 1.6 x 10(-6) for Pfu DNA polymerase, a greater than tenfold improvement over the 2.0 x 10(-5) error rate for Taq DNA polymerase, after approx. 10(5)-fold amplification.

Expression of a heterodimeric Fab antibody protein in one cloning step.

A new method is presented for creating antibody expression libraries in Escherichia coli. Rather than perform two cloning steps to express the heavy and light chains of the antigen binding domain, we have used a fusion-PCR method to link the coding regions for heavy and light chain sequences in a single DNA molecule prior to vector ligation. This greatly simplifies the construction of antibody expression clones.

Transfection of a factor-dependent cell line with the murine interleukin-3 (IL-3) cDNA results in autonomous growth and tumorigenesis.

The factor dependent murine myeloid line 32D c15 was transfected by electroporation with a murine interleukin-3 (IL-3) cDNA expression plasmid bearing the murine metallothionein-I promoter element. Factor-independent cell growth was readily obtained, and was shown to be accompanied by the production of biologically active IL-3. Three cell lines, growing autonomously and secreting IL-3 activity into their supernatants were established. S-1 nuclease analysis was employed to demonstrate that the introduced plasmid and not the endogenous IL-3 gene was the source of the IL-3 in one of these lines. The transfected IL-3 secreting cell lines, but not the parental factor-dependent 32D c15 cells, were uniformly able to induce tumors in syngeneic mice. These results indicate that the conversion to a malignant phenotype of a "partially transformed" cell line may be achieved by one additional dominant genetic event, such as the acquisition of autocrine growth factor secretion.

Congenital endodermal heterotopia of the atrioventricular node: evidence for the endodermal origin of so-called mesotheliomas of the atrioventricular node.

A case of so-called mesothelioma of the atrioventricular node is presented. Controversy exists as to whether this lesion is of mesodermal or endodermal origin. The light and electron microscopic morphologic characteristics in this case were identical to those reported previously. The glandular component produced mucin that resisted digestion with both hyaluronidase and diastase; this staining pattern is characteristic of endodermal rather than of mesodermal tissue. Immunohistochemical methods demonstrated abundant carcinoembryonic antigen (CEA) in the cytoplasm of the cells composing the lesion. The presence of CEA strongly argues for an endodermal origin, since this antigen characterizes tissue derived from endoderm and is generally absent from mesoderm. The lesion probably represents endodermal foregut tissue that is displaced during embryogenesis. As such, it is not a true neoplasm. It is proposed that this lesion be designated "congenital endodermal heterotopia of the atrioventricular node."

Analysis of spontaneous and induced mutations in transgenic mice using a lambda ZAP/lacI shuttle vector.

A short term, in vivo mutagenesis assay has been developed utilizing a lacl target gene contained within a lambda ZAP shuttle vector which has been incorporated into transgenic mice. Following chemical exposure, the target gene was recovered from mouse genomic DNA by mixing the DNA with in vitro lambda phage packaging extract. Mutations within the lacl target were identified by infecting host E. coli with the packaged phage and plating on indicator plates containing Xgal. Phage plaques with mutations in the lacl appeared blue, while intact phage were colorless. The ratio of blue plaques to colorless plaques is a measure of the mutagenicity of the compound. This system was used to obtain significant induction (up to 74-fold) over background levels for a variety of compounds, including N-ethyl-N-nitrosourea, benzo(a)pyrene (BaP), cyclophosphamide, and methylnitrosourea. Sequence analysis of selected mutant clones derived from this system was accomplished through the use of partial filamentous phage origins which allow rapid transfer of the target gene from phage to plasmid. Sequence analysis of spontaneous mutants derived from the mice primarily found of base substitutions, differing markedly from the previous data for spontaneous mutations in lacl derived from E. coli, where the preponderance of mutations were found at a single site, a repeated tetramer sequence. Upon sequence analysis of BaP derived base substitutions, only transversions were obtained, consistent with the known mechanism of BaP mutagenesis. Use of the well-characterized lacl gene in transgenic mice should allow for extrapolation of the extensive pool of in vitro data to whole animals, as well as provide insight into the tissue specific effects of mutagenic compounds.

The lesson from cancer pain.

The success of the WHO guidelines for the treatment of cancer pain indicates that cancer pain was previously undertreated. At the heart of these guidelines lies the three-step analgesic ladder, the last two steps of which consist of prescribing opioids. Today, the use of opioids in cancer patients is generally accepted, but there are still some concerns over the risks of addiction and adverse reactions, and opioids are sometimes withheld from patients who would otherwise benefit from them. However, it has been shown that such concerns are misplaced: the risks of severe adverse reactions and addiction are low when opioids are used correctly in patients with chronic pain. The use of opioids to treat benign pain is even less widely accepted in many countries, despite recommendations that they should be prescribed. It is emphasized that the use of opioids is a valid option for treating benign pain, and they should not be withheld from patients who need them. Opioids are always indicated when other therapeutic options, including NSAIDs, have failed or are contraindicated. When opioids are prescribed, procedures should be followed to provide the patient with maximum benefit and minimum risk.

Hepatocarcinogenesis (Z#2)/mutagenesis during initiation stage.

Previously, we developed a model for high incidence, endogenously generated hepatocellular carcinoma (HCC), the human alpha-1-antitrypsin (alpha1AT) Z gene transgenic mouse (Z#2). We now examine the potential utility of a model for endogenous carcinogenesis utilizing the Z#2 mouse also transgenic for the lacI gene, a convenient target for in vivo mutagenesis studies. We crossed the Z#2 line and mice transgenic for lambda/lacI shuttle vector (Big Blue), for determination of lacI mutant frequency during initiation of endogenous carcinogenesis. Five month old double transgenic mice (Z#2+/lacI+) successfully displayed: (1) the expected post-inflammatory stage of Z#2 carcinogenesis; and (2) hepatic lacI mutants measured at frequencies (10(-5)-10(-4)) useful to mutagenesis studies. In this study, hepatic lacI mutation frequencies in Z#2 transgenic mice appeared to be only slightly increased (< 2x) when compared to age matched negative controls. In the future, it may be important to reconcile possibly limited lacI mutagenesis at the time of initiation and demonstrated high incidence of hepatocarcinogenesis.

Carcinomas metastatic to follicular adenomas of the thyroid gland. Report of two cases.

Metastases to the thyroid gland are an uncommon occurrence, and metastasis to a preexisting thyroid neoplasm is even more rare. We report two cases of tumor-to-tumor metastasis where a prostatic and a breast carcinoma metastasized to follicular adenoma of the thyroid gland. The metastatic process in case 1 was initially diagnosed by fine-needle aspiration biopsy and later confirmed with the hemithyroidectomy. Immunostaining for prostate-specific antigen and prostatic acid phosphatase in case 1 and estrogen and progesterone receptors in case 2 demonstrated strong immunoreactivity in the metastatic tumor cells. Flow cytometric DNA analysis of the primary and the metastatic tumors in both cases demonstrated stemline fidelity that supported their association. Our cases exemplify why attention should be given to the possibility of metastasis when distinctly different morphologic features are seen in an otherwise typical tumor and the utility of ancillary tests that may assist in establishing the diagnosis.

[Long-term therapy of tumor pain using morphine-retard tablets]. / Langzeittherapie von Tumorschmerzen mit Morphin-retard-Tabletten.

We analysed the effect of sustained-release morphine tablets in 174 patients with severe cancer pain. A good relief of pain could be obtained in 65% of the patients within the first week and in 80% of the patients at the end of therapy. The mean daily dose was at 178 mg morphine, six patients needed more than 1000 mg per day. The sustained-release morphine was given at fixed intervals, in 80% of the cases every eight hours. No severe side-effects were associated with long-term morphine therapy. We often saw nausea and vomiting, constipation and drowsiness, but these side-effects decreased after the first weeks of treatment. Only in ten patients we had to stop therapy because of side-effects. Morphine can be used successfully in the treatment of cancer pain for long periods without concern about tolerance.