Endogenous retroviral LTR DNA sequences as markers for individual human chromosomes

Two groups of endogenous MMTV related retroviral env transcripts expressed in human tissues

The human genome contains at least 50 copies of the human endogenous retrovirus K (HERV-K) family which is related to the mouse mammary tumor virus (MMTV). Some members have been shown to be transcriptionally active and to have large open reading frames. Using the RT-PCR method we have investigated the HERV-K env transcription pattern in several malignant tissues and in peripheral blood mononuclear cells PBMCs). Samples were derived from chronic myelogenous leukemia (CML), breast cancer, colon cancer, high and low grade non-Hodgkin's lymphomas, Hodgkin's disease, myelodysplastic syndrome, thyroid adenoma (TA) and from PBMCs of patients with breast cancer, gastric cancer, and of healthy individuals. We found abundant HERV-K env transcripts in all tissues under investigation. Using HERV-K 10 specific primers for amplification we detected in addition to transcripts with high homology to HERV-K 10 (ca. 96% homology on the amino acid level) also transcripts of low homology to HERV-K10 (ca. 71%). Interestingly, all solid tissues containing high percentages of malignant cells such as breast cancer, colon carcinoma, low and high grade non-Hodgkin's lymphomas showed exclusively HERV-K env related transcripts with low homology to HERV-K 10. In contrast, in samples containing only a low proportion of malignant cells or no malignant cells at all we observed both types of transcripts. Thus, our data suggest that the expression pattern of HERV-K elements in human cells is very heterogenous and subjected to a complex transcriptional regulation.

Distribution of human endogenous retroviral RTVL-H2 LTR sequences among human chromosomes

The human genome carries multiple copies of sequences related to endogenous retroviral DNA. We report here the distribution of a new multicopy long terminal repeat (LTR) sequence that has been a part of an endogenous retrovirus-like sequence RTVL-H2. Twenty-four human chromosomes were either separated by flow sorting or by using rodent cells carrying a single human chromosome, and the DNA was subjected to Southern analyses using the RTVL-H2 DNA as a probe. The RTVL-H2 LTRs were distributed among all the human chromosomes, but the density and the profile differed from chromosome to chromosome. The same chromosome obtained from different individuals showed essentially the same chromosome-specific patterns. The distribution of the RTVL-H2 LTRs among different chromosomes did not correlate with the distribution of LTRs from another endogenous retroviral DNA, HERV-A, strongly suggesting that there is no preferred chromosome or a region thereof, for the integration. The possibility of rearrangement or amplification after integration is discussed.

Segmental genomic replacement by Cre-mediated recombination: genotoxic stress activation of the p53 promoter in single-copy transformants

Genotoxic stress results in transcriptional activation of the p53 promoter. To gain more detailed information on genotoxic induction of the p53 promoter at a uniform genomic locus, we have developed an efficient strategy for replacing a defined genomic segment in mouse NIH 3T3 cells with exogenous transfected DNA using a 'double lox' targeting strategy mediated by Cre DNA recombinase. The strategy utilizes a pair of heterospecific lox sites engineered both into the genome and onto the targeting DNA. This allows direct replacement of genomic DNA by a Cre-catalyzed double crossover event. p53-CAT reporter constructs were site-specifically placed into the genomic target 20-fold more efficiently by double lox recombination than by Cre-mediated single crossover insertional recombination, and the absolute frequency of site-specific double lox targeting exceeded the frequency of transformation due to random illegitimate recombination of transfected DNA into the genome. Resulting targeted single-copy integrants of the p53-CAT reporter show strong genotoxic induction by mitomycin C, and a dynamic range of induction that exceeds that seen in transient transfection assays. The double lox strategy is generally applicable to Cre-mediated genomic targeting in any cell and should be of particular utility in the site-specific targeting of DNA into embryonic stem (ES) cells for the production of gene-modified mice.

Evolution and biological significance of human retroelements

Retroelements comprise a substantial portion of the human genome. Their large number and ubiquitous distribution has led scientists to speculate about their evolutionary origin and their biological functions. Human endogenous retroviruses and their retrotransposon relatives represent a reservoir of possibly pathogenic retroviral genes that may be activated spontaneously or by environmental conditions. They can act as insertion mutagens and activate or inactivate cellular genes, or may be involved in chromosome aberrations by recombination of related elements on different chromosomal locations. Retroviral gene products themselves may also be pathogenic and, for example, could be implicated in the development of tumors and autoimmune diseases. On the other hand, endogenous retroviral elements and nonviral retroposons are thought to have played an important role in shaping the genomes of vertebrates by intracellular transposition events and by generating hot spots of recombination. In the course of time, some of these elements have acquired cellular functions, such as, for instance, in the regulation of gene expression. Therefore, the role of human endogenous retroviruses and retroposons in biological processes is currently a subject of great interest.

Cloning and characterization of the endogenous retroviral-tRNA(Glu) multigene family from human genomes of different racial backgrounds

An 8.3-kb human endogenous retroviral-tRNA(Glu) (HERV-E)-encoding cDNA clone and a 1.5-kb genomic clone were isolated from a Chinese-derived cervical cancer cell line, CC7T, and their sequences determined. The former is a full-length endogenous retroviral cDNA containing corresponding u5-gag-pol-env-u3-r regions. The latter is a partial retroviral DNA segment, covering the gag and pol genes. Analysis of normal human DNA by Southern blot hybridization with three specific HERV-E molecular DNA probes revealed complex restriction-fragment length polymorphisms (RFLP), implying that the human genome contains diverse proviral structures and dispersed integration sites. The complex patterns were virtually identical between DNAs from African-Americans, Asians and Caucasians, with only a few minor variations. The data suggest that these proviral sequences were mostly incorporated into the human genome before racial divergence and, hence, may serve as markers for distinct chromosomal sites.

Is a positive western blot proof of HIV infection?

It is currently accepted that a positive Western blot (WB) HIV antibody test is synonymous with HIV infection and the attendant risk of developing AIDS. In this communication we present a critical evaluation of the presently available data on HIV isolation and antibody testing. This evidence indicates that: (1) the antibody tests are not standardized; (2) the antibody tests are not reproducible; (3) the WB proteins (bands) which are considered to be encoded by the HIV genome and to be specific to HIV may not be encoded by the HIV genome and may in fact represent normal cellular proteins; (4) even if the proteins are specific to HIV, because no gold standard has been used to determine specificity, a positive WB may represent nothing more than cross-reactivity with non-HIV antibodies present in AIDS patients and those at risk. We conclude that the use of antibody tests as a diagnostic and epidemiological tool for HIV infection needs to be reappraised.

Genomic targeting with purified Cre recombinase

Purified Cre recombinase protein introduced directly into cultured mammalian cells by lipofection catalyzes both site-specific chromosomal integration of a co-transfected lox targeting vector and precise excision of genomic DNA flanked by directly repeated lox sites. This procedure eliminates the need to transfect cre expression plasmids to activate recombination at lox sites. We used this simplified procedure to investigate the effect on targeting efficiency of both lox vector design and chromosomal position of the lox target. We show that such chromosomal position effects can exert at least a 50-fold per lox target difference in targeting efficiency in a human osteosarcoma cell line.

Genomic targeting with a positive-selection lox integration vector allows highly reproducible gene expression in mammalian cells

Stable transformants of mammalian cells from gene transfer often show extreme variability in expression of the introduced transgene. This occurs from the highly variable number of copies integrated into the genome and from position effects on gene expression due to random integration. We have eliminated both of these constraints on predictable gene expression by use of a lox recombination vector. The positive selection vector system is designed to directly select Cre-mediated DNA integration at a lox target previously placed into the genome of cultured mammalian cells. Proper targeting activates expression of a defective lox-neomycin phosphotransferase (neo) fusion gene target. With CHO cell lines containing this target, almost all of the selected transformants (54 of 56 independent G418-resistant colonies) were simple single-copy integrants of the targeting DNA. To monitor gene expression at a single chromosomal site, we used a beta-actin promoter-lacZ reporter construct. Independent G418-resistant colonies from site-specific integration of the reporter gene all showed nearly identical levels of beta-galactosidase activity when the reporter construct integrated at a particular chromosomal position. The same construct integrated at a second chromosomal position exhibited a slightly different level of activity, characteristic of that second position. These results show that Cre-mediated site-specific integration can facilitate the construction of isogenic cell lines and thereby permit reproducible gene expression in stably transformed cell lines.

Banding profiles of LTR of human endogenous retrovirus HERV-A in 24 chromosomes in somatic cell hybrids

The human genome carries multiple copies of sequences related to endogenous retroviral genomes. We investigated the distribution of one of these sequences, HERV-A, in 24 human chromosomes by Southern analyses using DNAs from flow-sorted chromosomes or rodent cells carrying a single human chromosome. The results showed that HERV-A is distributed among all human chromosomes and that each chromosome has a specific Southern blot profile. The chromosome-specific pattern did not show significant polymorphism, except in a few cases, when the same chromosome obtained from different individuals was compared. These chromosome-specific Southern hybridization profiles may be useful for chromosome karyotyping. This would allow the integrity of human chromosomes in human-rodent somatic cell hybrids to be monitored without using conventional cytogenetic methods.

AIDS acquired by drug consumption and other noncontagious risk factors

The hypothesis that human immunodeficiency virus (HIV) is a new, sexually transmitted virus that causes AIDS has been entirely unproductive in terms of public health benefits. Moreover, it fails to predict the epidemiology of AIDS, the annual AIDS risk and the very heterogeneous AIDS diseases of infected persons. The correct hypothesis must explain why: (1) AIDS includes 25 previously known diseases and two clinically and epidemiologically very different epidemics, one in America and Europe, the other in Africa; (2) almost all American (90%) and European (86%) AIDS patients are males over the age of 20, while African AIDS affects both sexes equally; (3) the annual AIDS risks of infected babies, intravenous drug users, homosexuals who use aphrodisiacs, hemophiliacs and Africans vary over 100-fold; (4) many AIDS patients have diseases that do not depend on immunodeficiency, such as Kaposi's sarcoma, lymphoma, dementia and wasting; (5) the AIDS diseases of Americans (97%) and Europeans (87%) are predetermined by prior health risks, including long-term consumption of illicit recreational drugs, the antiviral drug AZT and congenital deficiencies like hemophilia, and those of Africans are Africa-specific. Both negative and positive evidence shows that AIDS is not infectious: (1) the virus hypothesis fails all conventional criteria of causation; (2) over 100-fold different AIDS risks in different risk groups show that HIV is not sufficient for AIDS; (3) AIDS is only 'acquired,' if at all, years after HIV is neutralized by antibodies; (4) AIDS is new but HIV is a long-established, perinatally transmitted retrovirus; (5) alternative explanations disprove all assumptions and anecdotal cases cited in support of the virus hypothesis; (6) all AIDS-defining diseases occur in matched risk groups, at the same rate, in the absence of HIV; (7) there is no common, active microbe in all AIDS patients; (8) AIDS manifests in unpredictable and unrelated diseases; and (9) it does not spread randomly between the sexes in America and Europe. Based on numerous data documenting that drugs are necessary for HIV-positives and sufficient for HIV-negatives to develop AIDS diseases, it is proposed that all American/European AIDS diseases, that exceed their normal background, result from recreational and anti-HIV drugs. African AIDS is proposed to result from protein malnutrition, poor sanitation and subsequent parasitic infections. This hypothesis resolves all paradoxes of the virus-AIDS hypothesis. It is epidemiologically and experimentally testable and provides a rational basis for AIDS control.