[Role of evidence-based medicine in intensive care]. / Rolle der evidenzbasierten Medizin in der Intensivmedizin.

Evidence-based medicine (EBM) plays an important role in intensive care. Along with the individual expertise of the attending physician and the preferences of the respective patient, recent study evidence is an important decision criterion when choosing the appropriate diagnostic and therapeutic procedures. Both a target-orientated literature search and adequate evaluation of the risk of bias as well as interpretation of the depicted outcomes are necessary to be able to draw the right conclusions from study results. Furthermore, proper publication formats might facilitate the synopsis of the available evidence and support the implementation of this knowledge in routine clinical work.

Simultaneous quantitation of perfluoroalkyl acids in human serum and breast milk using on-line sample preparation by HPLC column switching coupled to ESI-MS/MS.

A high throughput analytical method using a column switching high-performance liquid chromatography combined with isotope dilution tandem mass spectrometry (column switching-HPLC-MS/MS) was developed to simultaneously quantitate the concentrations of 7 perfluoroalkyl acids (PFAAs) in serum and 3 PFAAs in breast milk samples. The sample preparation includes addition of the isotope-labelled internal standard solution to breast milk and serum, enzymatic hydrolysis and filtration of milk samples, precipitation of proteins and analysis by column switching-HPLC-MS/MS. The limits of quantitation ranged from 0.1 to 0.4 µg/l for serum and 0.02 to 0.15 µg/l for breast milk samples. The method accuracies ranged between 73.2% and 100.2% for the different analytes at two concentrations in PFAAs spiked samples. The validity of the method was confirmed by analysing 20 serum and 20 breast milk samples.

Abyss1: a novel L2-like non-LTR retroelement of the snakelocks anemone (Anemonia sulcata).

Non-LTR retrotransposons are a diverse and taxonomically widely dispersed group of retroelements that can be divided into at least 14 distinguishable clades. Basal metazoans have not been examined in great detail for their retrotransposon content. In order to screen for the presence of reverse transcriptase (RT) related sequences in Cnidaria and Ctenophora, basal phyla of metazoans, PCR with highly degenerate oligonucleotides was performed and an RT-like sequence was identified from the sea anemone species Anemonia sulcata. Further screening identified a related element in another anemone species Actinia equina. Significant homology to non-LTR retrotransposon RTs was observed, particularly to L2-like elements of fish such as Maui. The sequence was not detected among other cnidarians and we have designated the A. sulcata and A. equina elements Abyss1 and Abyss2 respectively. Phylogenetic analysis of Abyss1 compared with members of 14 known non-LTR retroelement clades suggests that the sequence represents a novel L2 element.

Functional activity of HERV-K-T47D-related long terminal repeats.

The human genome contains a family of endogenous retroviruses, HERV-K(HML-4), that comprises the full-length provirus HERV-K-T47D, five related elements, and hundreds of solitary long terminal repeats (LTRs). We here show that HERV-K-T47D-related LTRs are dispersed over all human chromosomes and have arisen after the divergence of Old and New World monkeys. By screening a cDNA library derived from the human mammary carcinoma cell line T47D with a HERV-K-T47D LTR probe, we isolated several clones containing LTR/cellular gene chimeras and assessed the transcriptional activity of these LTRs in transient transfection experiments. All LTRs were able to drive the expression of a reporter gene, thereby displaying distinct activities in different cell lines. We found that sequences located downstream of the LTR-U3 region modulate the level of gene expression. Based on the impact of the R region we distinguished between three different LTR types; the activity of type I LTRs was enhanced in the presence of the LTR-R region in all cell lines tested, whereas a type II LTR was downregulated. Type III LTRs are characterized by lacking or having a varying influence of the R region that was dependent on the cell line used. Finally, our results attribute to LTR-U5-gag sequences a role in determining LTR activity.

Cell type-specific expression and promoter activity of human endogenous retroviral long terminal repeats.

Evolution over millions of years has adapted several thousand copies of retrovirus-like elements and over 10 times as many solitary long terminal repeats (LTRs) to their present location in the human genome. Transcription of these human endogenous retroviruses (HERVs) has been detected in various cells and tissues, and in some cases their transcriptional control elements have been recruited by cellular genes. We used a retroviral pol-specific expression array to obtain a HERV transcription profile in a variety of human cells such as epidermal keratinocytes, liver cells, kidney cells, pancreatic cells, lymphocytes, and lung fibroblasts. This rapid screening test revealed a distinct HERV pol-expression pattern in each cell type tested so far. About 40 different U3/R regulatory sequences from the HERV-H and HERV-W families were then amplified from actively transcribed 3'HERV LTRs of various cell lines and tissues. Their promoter activities were compared with LTR sequences of other known HERV families in 12 human cell lines using a transient luciferase reporter system. Expression of the isolated HERV LTRs varied significantly in these cell lines, in some cases showing strict cell type specificity. These results suggest that endogenous retroviral LTRs may be a valuable source of transcriptional regulatory elements for the construction of targeted retroviral expression vectors.

HERV-K-T47D-Related long terminal repeats mediate polyadenylation of cellular transcripts.

The human genome harbors thousands of long terminal repeats (LTRs) that are derived from endogenous retroviruses and contain elements able to regulate the expression of neighboring cellular genes. We have investigated the ability of human endogenous retroviral (HERV)-K LTRs to provide transcriptional processing signals for nonviral sequences. Four chimeric cDNA clones isolated from a cDNA library derived from the human cell line T47D were found to be polyadenylated within an HERV-K-T47D-related LTR. Two transcripts containing an as yet unknown cellular sequence were probably derived from the same genomic locus but their 3' ends were processed at different positions of the LTR. Structural analysis of the polyadenylation site suggests RNA stem-loop structures similar to the HTLV-1 Rex responsive element that bring the two remote AAUAAA and GU-rich elements into the spatial juxtaposition necessary for correct 3' end processing. The cellular part of the third chimeric clone shows significant homology to an exon of the human tyrosine phosphatase 1 gene, although oriented in the antisense direction compared to the adjacent LTR. Furthermore, we found that the 3' untranslated region of the human transmembrane tyrosine kinase gene FLT4 is probably derived from a partial HERV-K-T47D LTR sequence. Taken together, our data suggest that LTRs of the HERV-K-T47D family display biological function by mediating polyadenylation of cellular sequences.

Rapid identification of all known retroviral reverse transcriptase sequences with a novel versatile detection assay.

We have developed a highly sensitive, universal assay that allows detection as well as identification of all known retroviral reverse transcriptase (RT)-related nucleic acids in a biological sample by a single two-step experiment. The assay combines polymerase chain reaction (PCR) and reverse dot-blot hybridization (RDBH), using an array of immobilized synthetic retrovirus-specific oligonucleotides and two sets of mixed oligo primers (MOPs). These primers were derived from highly conserved motifs found in all known reverse transcriptase genes. The PCR/RDBH assay was used for qualitative analyses of human endogenous retrovirus (HERV) transcription in peripheral blood mononuclear cells (PBMCs) and in particles released by the human mammary carcinoma-derived cell line T47D. Sensitivity was further demonstrated by detection of down to 10 copies of pig endogenous retrovirus (PERV) DNA in human cDNA samples. Therefore, this assay is particularly useful for the identification of retroviral sequences in xenografts as well as in recipients of xenografted tissues and organs. Moreover, it is a valuable tool to detect retroviral transcripts and particles in cell cultures used for production of therapeutic polypeptides. The assay is further suitable for monitoring vector preparation used in human gene therapy to exclude transfer of copackaged endogenous retroviruses into target cells.

Solitary HERV-K LTRs possess bi-directional promoter activity and contain a negative regulatory element in the U5 region.

Reporter gene analysis of HERV-K solitary long terminal repeats (LTRs) showed that they retain detectable activity in human teratocarcinoma cells, and can direct the transcription in both orientations relative to the reporter gene. Deletion analysis demonstrated the possible existence of alternative promoters within the LTR as well as a silencer-like element in the U5 region. Our results indicate also that all-trans-retinoic acid is capable of modulating expression of the reporter gene directed by a HERV-K LTR in NT2/D1 cells.

HERV-IP-T47D, a novel type C-related human endogenous retroviral sequence derived from T47D particles.

A new type C retrovirus-related endogenous pol sequence (ERV-FTD) found to be occasionally copackaged in retrovirus-like particles released by the human mammary carcinoma cell line T47D was used to screen a human genomic library (Seifarth W, Skladny H, Krieg-Schneider F, Reichert A, Hehlmann R, and Leib-Mösch C: J Virol 1995;69:6408-6416). The DNA sequence of one full-length clone now reveals a human endogenous proviral sequence (HERV) of 4190 bp in length comprising a 5' LTR (489 bp) and regions with 37 and 74% overall amino acid homology to RTVL-Ia gag and pol genes, respectively. About 35 related elements were found to be distributed on all human chromosomes except 16, 17, and Y. Sequence comparisons with Mo-MuLV and various type C-related HERVs suggest that despite a proline primer-binding site this novel HERV element, now named HERV-IP-T47D, can be assigned to one family together with known HERV-I elements. Phylogenetic analyses of 5 proviral and 25 solitary LTR sequences confirmed the existence of two distinct but closely related subgroups of the HERV-IP superfamily in the primate genome. In contrast to most known HERV-families, the evolutionary age of HERV-IP elements dates back prior to the divergence of New and Old World monkeys. Despite their old age, members of the HERV-IP family are still transcriptionally active and were found to be highly expressed in specific human tissues such as liver and kidney.

Specific detection of Aspergillus species in blood and bronchoalveolar lavage samples of immunocompromised patients by two-step PCR.

The increasing incidence of aspergillosis, a life-threatening infection in immunocompromised patients, emphasizes the need to improve the currently limited diagnostic tools. We developed a two-step PCR assay that specifically amplifies a region of the 18S rRNA gene that is highly conserved in Aspergillus species. A number of primers with the least homology to equivalent human or Candida gene sequences were screened for the pairs that gave the highest sensitivity and specificity. No cross-reaction with the wide range of fungal and bacterial pathogens so far tested was observed. This assay allows direct and rapid detection of down to 10 fg of Aspergillus DNA corresponding to 1 to 5 CFU per ml of blood. A total of 315 blood and bronchoalveolar lavage samples from 140 subjects, including 93 patients at risk for invasive fungal disease, were screened. The result was a 100% correlation between positive histology, culture, or high-resolution computed tomography findings and PCR results. The test specificity was 89%. Our data point to the considerable potential clinical value of this simple, specific, rapid, and inexpensive PCR assay for improving the means of early diagnosis of systemic aspergillosis in high-risk patients.

Transcriptional activation of endogenous retroviral sequences in human epidermal keratinocytes by UVB irradiation.

Ultraviolet radiation is a pathogenic factor in various diseases, e. g., autoimmune disorders such as lupus erythematosus. On the other hand, endogenous retroviruses are discussed as etiologic agents in lupus erythematosus. Therefore, we investigated the influence of ultraviolet irradiation on expression of human endogenous retroviral sequences and human endogenous retroviral sequence promoter-driven transcription of cellular genes using human epidermal keratinocytes as a model system. First, conserved sequences of endogenous retroviral pol genes were amplified from cellular mRNA by reverse transcriptase polymerase chain reaction with degenerate oligonucleotide primers. Polymerase chain reaction products were hybridized in a reverse dot blot hybridization assay to a representative number of distinct cloned human endogenous retroviral pol fragments. Using this method, we could show that irradiation with 30 mJ per cm2 ultraviolet B activates transcription of various endogenous retroviral pol sequences in primary epidermal keratinocytes as well as in a spontaneously immortalized keratinocyte cell line (HaCaT). Interestingly, some of these sequences were found to be closely related to pol sequences of human endogenous retroviral sequences which have been shown to be expressed in autoimmune patients. Analysis of human endogenous retroviral pol expression in vivo using skin biopsies of lupus erythematosus patients revealed similar activation patterns. In a second approach, ultraviolet B- induced chimeric transcripts were isolated which are initiated by human endogenous retroviral promoters and proceed into cellular sequences using a newly established modified differential display polymerase chain reaction technique. The activation of human endogenous retroviral sequence transcription by ultraviolet B may contribute to the pathogenesis of lupus erythematosus, where inappropriate antigenic presentation of ultraviolet B-induced viral and cellular proteins could stimulate autoantibody production.

Proviral structure, chromosomal location, and expression of HERV-K-T47D, a novel human endogenous retrovirus derived from T47D particles.

We previously described that type B retrovirus-like particles released from the human mammary carcinoma cell line T47D are pseudotypes and package retroviral RNA of different origins (W. Seifarth, H. Skladny, F. Krieg-Schneider, A. Reichert, R. Hehlmann, and C. Leib-Mösch, J. Virol. 69:6408-6416, 1995). One preferentially packaged retroviral sequence, ERV-MLN, has now been used to isolate the corresponding full-length provirus from a human genomic library. The 9,315-bp proviral genome comprises a complete retroviral structure except for a 3' long terminal repeat (LTR) truncation. A lysine tRNA primer-binding site and phylogenetic analyses assign this human endogenous retroviral element, now called HERV-K-T47D, to the HML-4 subgroup of the HERV-K superfamily. The gag, prt, pol, and env genes exhibit 40 to 60% amino acid identity to HERV-K10. HERV-K-T47D is located on human chromosome 10, with five closely related elements on chromosomes 8, 9, 15, 16, and 19 and several hundred HERV-K-T47D-related solitary LTRs dispersed over the human genome. HERV-K-T47D-related sequences are detected in the genomes of higher primates and Old World monkeys but not in those of New World monkeys. High HERV-K-T47D transcription levels were observed in human placenta tissue, whereas transcription in T47D cells was strictly steroid dependent.

Mapping of a mouse mammary tumor virus integration site by retroviral LTR--arbitrary polymerase chain reaction.

The de novo integration of retroviral genomes within the mammalian genome is believed to contribute to the tumorigenic process. Integration may result in the disruption or inappropriate transcription of key regulatory genes. We describe the application of an arbitrarily primed PCR method for the mapping and cloning of genomic integration sites of the mouse mammary tumor virus (MMTV). We have amplified DNA sequences between a selected retroviral MMTV-LTR and random sites in the 3' flanking DNA. Using this technique we were able to visualize several proviral integration sites present in a MMTV-induced mammary tumor derived cell line that were absent from the germ line. Cloning and sequencing of the PCR product corresponding to one site established its identification as an unique 3' flanking sequence.

Identification of endogenous retroviral sequences based on modular organization: proviral structure at the SSAV1 locus.

The current genome sequencing projects reveal megabases of unknown genomic sequences. About 1% of these sequences can be expected to be of retroviral origin. These are often severely deleted or mutated. Therefore, identification of the retroviral origin of these sequences can be very difficult due to the absence of convincing overall sequence similarity. There are also many copies of solo-LTRs (long terminal repeats) distributed throughout genomic sequences. LTR and envelope sequences in general are among the most divergent parts of the retroviral genome and thus especially hard to detect in mutated endogenous sequences. We took advantage of the fact that these retroviral sections contain short highly conserved sequence regions providing retroviral hallmarks even after loss of overall similarity. We defined several sequence elements and peptide motifs within LTR and Env sequences and used these elements to construct models for LTRs and Env proteins of mammalian C-type retroviruses. We then used this strategy to identify successfully the hitherto missing LTRs and an env-like region in the S71 human retroviral sequence. Our approach provides a new strategy for identifying remotely related retroviral sequences in genomic DNA (especially human DNA), of potential significance for the interpretation of genomic sequences obtained from the current large-scale sequencing projects.

Endogenous retroviral sequences in the pathogenesis of systemic autoimmune disease.

OBJECTIVES: To update information on endogenous retroviral sequences and discuss their role in systemic autoimmune disease. DATA SOURCES: Articles retrieved after MEDLINE search and personal communications and cooperation with the Institute of Virology. DATA SYNTHESIS: There are 2 modes of pathogenetic mechanisms through which endogenous retroviral sequences could cause systemic autoimmune disease: expression of endogenous retroviral gene products sharing antigenic determinants with cellular proteins; and activation or destruction of cellular genes as a consequence of insertional mutagenesis. Both mechanisms have been demonstrated in vitro and in vivo in animal models. CONCLUSION: Investigations on endogenous retroviral sequences in humans may offer new insights into the pathogenesis of autoimmune disease.

Randomized studies with interferon in chronic myelogenous leukemia (CML) and comparative molecular aspects. German CML Study Group.

Four randomized prospective studies on interferon alpha (IFN) in CML report varying degrees of prolongation of the chronic phase of CML and of survival as compared to conventional therapies. There is agreement that IFN prolongs survival as compared to standard busulfan. There is disagreement, however, as to which degree IFN is superior to hydroxyurea. Whereas the randomized studies of the Italian cooperative group and of the British MRC find a statistically significant survival advantage of IFN over hydroxyurea of about 20 months, this difference is only 10 months in the German randomized study and not significant. One reason for this difference might be the more intensive treatment schedule for the hydroxyurea control group in the German study. Other reasons might be differences in risk profiles between the patient groups studied and in strategies of IFN therapy. About 1% of the human genome consists of retroviral or retroviral-like sequences. By analogy to animal models, endogenous retroviruses might also have pathogenic potential in human disease. The transposon-like structure of retroviruses that enables them to integrate at almost any position in the host genome and the capability of retroviruses to serve as efficient vehicles of cellular genes are in support of a pathogenic potential. Furthermore, particles resembling retroviruses have been observed long ago in human embryonic and malignant tissues and cell lines. Sequence information and the transcriptional activity of the endogenous sequences argue against the possibility that these sequences are only fossil relics of early evolutionary periods. Most of the sequences appear to be inactivated by stop codons or frameshifts, making the genomic localization of open reading frames with biological activity difficult. Up to now, mutagenesis by insertion of retroviral-like sequences in sporadic cases of human disease appears to be the only example of pathogenic relevance of retroviruses in man.