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PubMed2003

Illegitimate DNA integration in mammalian cells.

Foreign DNA integration is one of the most widely exploited cellular processes in molecular biology. Its technical use permits us to alter a cellular genome by incorporating a fragment of foreign DNA into the chromosomal DNA. This process employs the cell's own endogenous DNA modification and repair machinery. Two main classes of integration mechanisms exist: those that draw on sequence similarity between the foreign and genomic sequences to carry out homology-directed modifications, and the nonhomologous or 'illegitimate' insertion of foreign DNA into the genome. Gene therapy procedures can result in illegitimate integration of introduced sequences and thus pose a risk of unforeseeable genomic alterations. The choice of insertion site, the degree to which the foreign DNA and endogenous locus are modified before or during integration, and the resulting impact on structure, expression, and stability of the genome are all factors of illegitimate DNA integration that must be considered, in particular when designing genetic therapies.

Animals↗
PubMed2004

Early B-cell factor-associated zinc-finger gene is a frequent target of retroviral integration in murine B-cell lymphomas.

The early B-cell factor (EBF)-associated zinc-finger protein (EBFAZ) binds to and negatively regulates EBF, a basic helix-loop-helix transcription factor required for B-cell lineage commitment and development of the olfactory epithelium. It also binds to SMA- and MAD-related protein 1 (SMAD1) and SMAD4 in response to bone morphogenic protein 2 (BMP2) signaling. It is highly related to ecotropic viral integration site 3 (EVI3), a protein that, like EBFAZ, contains 30 Krüppel-like zinc-finger repeats. In previous studies, we showed that Evi3 is a frequent target of retroviral integration in AKXD27 B-cell lymphomas. Here, we show that EBFAZ is also a frequent target. Integrations at Ebfaz and Evi3 are mutually exclusive, suggesting that they function in the same tumor pathway. Lymphomas with integrations at Ebfaz or Evi3 express the pre-B-cell-specific marker immunoglobulin lambda chain 5, and contain immunoglobulin heavy-chain rearrangements, suggesting that they are blocked at an early B-cell stage. Unlike Evi3, which is expressed at low levels in normal B cells, or Ebfaz, which is not expressed in B cells, both genes are highly expressed following viral integration. Collectively, our results suggest that ectopic expression of Ebfaz can substitute for the upregulated expression of Evi3 in B-cell disease and highlight the importance of this gene family in hematopoietic cancer.

Amino Acid Sequence↗
PubMed1998

Oligoclonal proliferation of human T-cell leukaemia virus type 1 bearing T cells in adult T-cell leukaemia/lymphoma without deletion of the 3' provirus integration sites.

We report a new case of an asymptomatic carrier with a deletion of a 3' HTLV-1 integration site. We further investigated whether these 3' deletions of flanking sequences may explain the oligoclonal pattern of HTLV-1 replication, evidenced by inverse PCR (IPCR) analysis of tumourous samples from patients with adult T-cell leukaemia (ATLL). 48 HTLV-1 3' integration sites, derived from tumourous DNA of five ATLL patients were sequenced. One dominant flanking sequence was obtained in the four samples harbouring a unique band after Southern-blotting. In one sample, which harboured two signals after Southern-blotting, IPCR amplification of diluted tumourous DNA revealed that these two sequences corresponded to one clone harbouring two integrated proviruses rather than to two distinct cellular clones, a result consistent with superinfection of the tumourous sample. In addition to integration sites corresponding to malignant clones, two to six oligoclonal forms were sequenced in four samples. No flanking sequence homology was found between clones derived from each patient, indicating that integration sites deletion in the vicinity of the provirus is a rare event in ATLL. The oligoclonal pattern of HTLV-1 replication in ATLL may result from clonal expansion of non-malignant HTLV-1-bearing clones within the sample and partly from HTLV-1 superinfection of monoclonal tumour cells.

Base Sequence↗
PubMed2000

Scientific misconduct and research integrity for the bench scientist.

This paper describes the role of the Office of Research Integrity (ORI), a component of the Public Health Service (PHS), in defining scientific misconduct in research supported with PHS funds and in establishing standards for responding to allegations of misconduct. The principal methods by which ORI exercises its responsibilities in this area are defining what types of behaviors undertaken by research investigators constitute misconduct, overseeing institutional efforts to investigate and report misconduct, and recommending to the Assistant Secretary for Health (ASH) PHS administrative actions when misconduct is identified. ORI also takes affirmative steps to promote research integrity through education, training, and other initiatives. The role of the research institution in responding to misconduct and promoting research integrity is complementary and overlapping with ORI's efforts but, as the employer of research investigators and front-line manager of the research, the institution has a greater opportunity to promote the highest standards of integrity in the day-to-day conduct of research. Finally, legal precedent established through civil litigation has played an important role in defining the standards that apply in determining when a breach of research integrity has occurred.

Academic Medical Centers↗
PubMed2005

The goals of comprehensive and integrated disease state management for diabetic kidney-disease patients.

Diabetes, cardiovascular disease, and chronic kidney disease present many challenges to clinicians as separate disease entities. Management and optimization of care of diabetic kidney-disease patients requires a proactive and integrated approach for all 3 disease states. To optimize the assessment, monitoring, and intervention in this population, comprehensive and integrated disease state management medical care plans must be established. Medical nutrition therapy is another key component that must be coordinated with these disease-state management medical care plans. Coordination of integrated disease-state management and medical nutrition therapy for diabetes, cardiovascular disease, and chronic kidney disease will help to improve patient outcomes and allow for a proactive approach to the identification, prevention, and management of potential disease-state complications. Several programs and guidelines have been established to accomplish these goals: the K/DOQI Clinical Practice Guidelines, the American Diabetes Association Standards of Medical Care for Diabetes (developed by the American Diabetes Association, the National Institute of Diabetes and Digestive Kidney Diseases, and the Centers for Disease Control-Diabetes Foundation), the National Diabetes Education Program, and the National Cholesterol Education Program. The multidisciplinary medical care team assumes an integral role in the success and implementation of this integrated approach as well as the empowerment of the patient in their own care.

Cardiovascular Diseases↗
PubMed2005

Symmetrical base preferences surrounding HIV-1, avian sarcoma/leukosis virus, and murine leukemia virus integration sites.

To investigate retroviral integration targeting on a nucleotide scale, we examined the base frequencies directly surrounding cloned in vivo HIV-1, murine leukemia virus, and avian sarcoma/leukosis virus integrations. Base preferences of up to 2-fold the expected frequencies were found for three viruses, representing P values down to <10(-100) and defining what appear to be preferred integration sequences. Offset symmetry reflecting the topology of the integration reaction was found for HIV-1 and avian sarcoma/leukosis virus but not murine leukemia virus, suggesting fundamental differences in the way different retroviral integration complexes interact with host-cell DNA.

Alpharetrovirus↗
PubMed2000

A phage integrase directs efficient site-specific integration in human cells.

The integrase from the Streptomyces phage phiC31 carries out efficient recombination between the attP site in the phage genome and the attB site in the host bacterial chromosome. In this paper, we show that the enzyme also functions in human cells. A plasmid assay system was constructed that measured intramolecular integration of attP into attB. This assay was used to demonstrate that in the presence of the phiC31 integrase, precise unidirectional integration occurs with an efficiency of 100% in Escherichia coli and >50% in human cells. This assay system was also used to define the minimal sizes of attB and attP at 34 bp and 39 bp, respectively. Furthermore, precise and efficient intermolecular integration of an incoming plasmid bearing attP into an established Epstein-Barr virus plasmid bearing attB was documented in human cells. This work is a demonstration of efficient, site-specific, unidirectional integration in mammalian cells. These observations form the basis for site-specific integration strategies potentially useful in a broad range of genetic engineering applications.

Bacteriophages↗
PubMed1987

Integration host factor is required for the DNA inversion that controls phase variation in Escherichia coli.

The on-and-off expression (phase variation) of type 1 fimbriae, encoded by fimA, in Escherichia coli is controlled by the inversion of a promoter-containing 314-base-pair DNA element. This element is flanked on each side by a 9-base-pair inverted, repeat sequence and requires closely linked genes for inversion. Homology analysis of the products of these genes, fimB and fimE, reveals a strong similarity with the proposed DNA binding domain of lambda integrase, which mediates site-specific recombination in the presence of integration host factor. Integration host factor, encoded by himA and hip/himD, binds to the sequence 5' TNYAANNNRTTGAT 3', where Y = pyrimidine and R = purine, in mediating integration-excision. In analyzing the DNA flanking the fim 314-base-pair inversion sequence, we found the adjacent sequence 5' TTTAACTTATTGAT 3', which corresponds perfectly with the consensus integration host factor binding site. To characterize the role of himA in phase variation, we transduced either a deletion of himA or an insertionally inactivated hip/himD gene into an E. coli strain with a fimA-lacZ operon fusion. We found the rate of phase variation decreases sharply from 10(-3) to less than 10(-5) per cell per generation. Southern hybridization analysis demonstrates that the himA mutation results in a failure of the switch-generated genetic rearrangement. When the transductant was transformed with a himA+ plasmid, normal switching returned. Thus integration host factor is required for normal type 1 fimbriae phase variation in E. coli.

Bacterial Adhesion↗
PubMed1992

Nonrandom integration of retroviral DNA in vitro: effect of CpG methylation.

We have developed a PCR-based system that allows us to assess the relative frequency of use of specific bases as targets for the avian leukosis virus in vitro integration system. Using this system, we tested the effect of 5-methylation of cytosine in runs of CpG on the distribution of integration target sites. We found that the distribution of preferred integration sites was not uniform along the target DNA; rather, there was a distinct and reproducible pattern of frequently used sites. This pattern was independent of orientation of the integrated DNA, and of overall structure and sequence of the target and fragment amplified. Methylation did not inhibit integration into CpG dinucleotides; on the contrary, this modification created highly preferred targets within runs of alternating CpG. Finally, similar but not identical specificity was observed by using preintegration complexes in infected extracts or purified integrase and DNA as enzyme and substrate. Thus, most of the specificity observed is conferred by interaction of integrase and targets, although it may be modified by other viral and/or cellular components.

Animals↗
PubMed1994

Adeno-associated virus (AAV) Rep proteins mediate complex formation between AAV DNA and its integration site in human DNA.

AAV is unique among eukaryotic viruses in the ability of its DNA to integrate preferentially into a specific region of the human genome. Understanding AAV integration may aid in developing gene therapy systems with predictable integration sites. Using a gel mobility-shift assay, we have identified a DNA sequence within the AAV integration locus on human chromosome 19 which is specifically bound by the AAV Rep78 and Rep68 proteins. This Rep recognition sequence is a GCTC repeating motif very similar to sequences within the inverted terminal repeats of the AAV genome which are also bound by Rep78 and Rep68. Cloned oligonucleotides containing the recognition sequence can direct specific binding by Rep proteins. Binding assays with mutant Rep proteins show that the amino-terminal portion of Rep78 and Rep68 can direct binding to either the AAV terminal repeat hairpin DNA or chromosome 19. This human genomic DNA can be complexed with AAV DNA by Rep proteins as demonstrated by a dual-label (32P/biotin) assay. These results suggest a role for Rep in targeting viral integration.

Bacterial Proteins↗
PubMed1996

Site-specific integration by adeno-associated virus.

Adeno-associated virus (AAV) has attracted considerable interest as a potential vector for gene delivery. Wild-type virus is notable for the lack of association with any human disease and the ability to stably integrate its genome in a site-specific manner in a locus on human chromosome 19 (AAVS1). Use of a functional model system for AAV DNA integration into AAVS1 has allowed us to conclude that the recombination event is directed by cellular DNA sequences. Recombinant junctions isolated from our integration assay were analyzed and showed characteristics similar to those found in latently infected cell lines. The minimal DNA signals within AAVS1 required for targeted integration were identified and shown to contain functional motifs of the viral origin of replication. A replication mediated model of AAV DNA integration is proposed.

Base Sequence↗
PubMed1998

The barrier-to-autointegration protein is a host factor for HIV type 1 integration.

In vivo, retroviral integration is mediated by a large nucleoprotein complex, termed the preintegration complex (PIC). PICs isolated from infected cells display in vitro integration activity. Here, we analyze the roles of different host cell factors in the structure and function of HIV type 1 (HIV-1) PICs. PICs purified by size exclusion after treatment with high salt lost their integration activity, and adding back an extract from uninfected cells restored this activity. In parallel, the native protein-DNA intasome structure detected at the ends of HIV-1 by Mu-mediated PCR footprinting was abolished by high salt and restored by the crude cell extract. Various purified proteins previously implicated in retroviral PIC function then were analyzed for their effects on the structure and function of salt-treated HIV-1 PICs. Whereas relatively low amounts (5-20 nM) of human barrier-to-autointegration factor (BAF) protein restored integration activity, substantially more (5-10 microM) human host factor HMG I(Y) was required. Similarly high levels (3-8 microM) of bovine RNase A, a DNA-binding protein used as a nonspecific control, also restored activity. Mu-mediated PCR footprinting revealed that of these three purified proteins, only BAF restored the native structure of the HIV-1 protein-DNA intasome. We suggest that BAF is a natural host cofactor for HIV-1 integration.

Animals↗
PubMed1996

Alternate strand DNA triple helix-mediated inhibition of HIV-1 U5 long terminal repeat integration in vitro.

Integration of the human immunodeficiency virus (HIV) DNA into the host genome is an obligatory process in the replicative life cycle of the virus. This event is mediated in vitro by integrase, a viral protein which binds to specific sequences located on both extremities of the DNA long terminal repeats (LTRs). These sites are highly conserved in all HIV genomes and thus provide potential targets for the selective inhibition of integration. The integrase-binding site located on the HIV-1 U5 LTR end contains two adjacent purine tracts on opposite strands, 5' . . . GGAAAATCTCT-3'/3'-CCTTTTAGAGA . . . 5', in parallel orientations. A single strand oligonucleotide 5'-GGTTTTTGTGT-3' was designed to associate with these tracts via its ability to form a continuous alternate strand DNA triplex. Under neutral pH and physiological temperature, the oligonucleotide, tagged with an intercalator chromophore oxazolopyridocarbazole, formed a stable triplex with the target DNA. The occurrence of this unusual triplex was demonstrated by both DNase I footprinting and electron microscopy. The triplex inhibits the two steps of the integrase-mediated reactions, namely, the endonucleolytic cleavage of the dinucleotide 5'-GT-3' from the 3' end of the integration substrate and the integration of the substrate into the heterologous target DNA. The midpoints for both inhibition reactions were observed at oligonucleotide concentrations of 50-100 nM. We believe that these results open new possibilities for the specific targeting of viral DNA LTR ends with the view of inhibiting integration under physiological conditions.

Base Sequence↗
PubMed2004

Histone H2AX is phosphorylated at sites of retroviral DNA integration but is dispensable for postintegration repair.

The histone variant H2AX is rapidly phosphorylated (denoted gammaH2AX) in large chromatin domains (foci) flanking double strand DNA (dsDNA) breaks that are produced by ionizing radiation or genotoxic agents and during V(D)J recombination. H2AX-deficient cells and mice demonstrate increased sensitivity to dsDNA break damage, indicating an active role for gammaH2AX in DNA repair; however, gammaH2AX formation is not required for V(D)J recombination. The latter finding has suggested a greater dependence on gammaH2AX for anchoring free broken ends versus ends that are held together during programmed breakage-joining reactions. Retroviral DNA integration produces a unique intermediate in which a dsDNA break in host DNA is held together by the intervening viral DNA, and such a reaction provides a useful model to distinguish gammaH2AX functions. We found that integration promotes transient formation of gammaH2AX at retroviral integration sites as detected by both immunocytological and chromatin immunoprecipitation methods. These results provide the first direct evidence for the association of newly integrated viral DNA with a protein species that is an established marker for the onset of a DNA damage response. We also show that H2AX is not required for repair of the retroviral integration intermediate as determined by stable transduction. These observations provide independent support for an anchoring model for the function of gammaH2AX in chromatin repair.

HeLa Cells↗
PubMed2003

Evaluation of the Tzu Chi Institute for Complementary and Alternative Medicine's Integrative Care Program.

OBJECTIVE: There are an increasing number of clinics providing integrative health care using new and innovative delivery models. The purpose of this study was to quantitatively and qualitatively evaluate the Integrative Care Program offered at the Tzu Chi Institute for Complementary and Alternative Medicine, Vancouver, British Columbia, Canada. DESIGN: At enrollment, data are collected on demographics, health history, current health concerns and diagnoses, quality of life/health status (SF-36) and patient satisfaction. The measures are repeated 6 months into the program. Descriptive analysis was used to summarize the data. Focus groups were also included as part of the study design. RESULTS: Patients seeking integrative care are a highly complex population living with numerous comorbid chronic conditions. Although their baseline scores on the SF-36 are lower than Canadian population norms across all subscales, significant improvement occurred from baseline to 6 months. Qualitative data support that patients were pleased with the clinical care they received and aligned with the philosophical underpinnings of the program. DISCUSSION: This is one of the first studies to evaluate integrative health care. Studies like this are needed to develop appropriate methods to assess models of integrative health care delivery.

Adult↗
PubMed2003

Alternative, complementary, and conventional medicine: is integration upon us?

In attempts to improve their health and/or combat illness, approximately 4 in 10 Americans will use a complementary and alternative medicine (CAM) therapy this year. CAM therapies vary widely, with acupuncture, chiropractic, herbal medicine, and homeopathy among the more prominent modalities. CAM therapies are used in addition to and/or instead of the more conventional forms of medical care available in U.S. hospitals or licensed physicians' offices. A rapidly increasing interest in CAM has led to a nascent movement aimed at integrating various CAM therapies with the conventional health care system. In Washington State, for example, health insurance coverage for CAM therapies has been mandated, and a number of "integrated" delivery systems have been born. Although the political and economic forces leading to adoption and integration of CAM therapies vary widely by geographic locale, it is likely that some degree of integration will occur throughout much of the United States. Similar processes are occurring in Canada, Europe, and Australia, and indeed within middle and upper level socioeconomic strata worldwide. This paper identifies potential barriers and facilitators to potential integration, of medical disciplines and argues for an accessible, multidisciplinary and evidence-based, yet humanistic and patient-oriented approach.

Australia↗
PubMed2003

Complementary and alternative medicine in mainstream public health: a role for research in fostering integration.

In light of the increased utilization of complementary and alternative medicine (CAM) in recent years, there is an increased possibility that CAM approaches could prove to be important factors in public health, particularly if used within an integrative framework together with mainstream medicine. There exists a defined need for research to explore the integration of conventional health care and CAM approaches, as well as define mechanisms of CAM-based therapies to facilitate such integration. Essential to these goals is the accumulation of a database derived from outcomes-based clinical and basic science investigations. We posit that that CAM clinicians need to be more thoroughly trained as researchers, skilled in developing and recording results of pragmatic studies that could provide credible evidence for the use of CAM in the public sector health care. It is proposed that this may be best achieved through a three-tiered system in which (1) clinician-scientists of both mainstream and alternative disciplines recognize the value of research designed to foster such integration; (2) educational and health care institutions must develop academic and clinical training programs that examine and delineate each disciplines' respective strengths and weaknesses; and (3) such programs are attractive to, and receive continued extramural subsidy. In the broadest sense, such a paradigmatic approach to CAM integration could create a common basis for scientific dialogue, encourage exchanges between medical communities, and establish policies for the development of a true multidisciplinary health care cooperative that is consistent with the current public health model.

Complementary Therapies↗
PubMed2002

Does an integrated care pathway improve processes of care in stroke rehabilitation? A randomized controlled trial.

OBJECTIVE: to evaluate whether integrated care pathways improve the processes of care in stroke rehabilitation. DESIGN: comparison of processes of care data collected in a randomized controlled trial. PARTICIPANTS: acute stroke patients undergoing rehabilitation randomized to receive integrated care pathways management (n=76) or conventional multidisciplinary care (n=76). MEASUREMENTS: proportion of patients meeting recommended standards for processes of care using a validated stroke audit tool. RESULTS: integrated care pathways methodology was associated with higher frequency of stroke specific assessments, notably testing for inattention (84% versus 60%; P=0.015) and nutritional assessment (74% versus 22%, P<0.001). Documentation of provision of certain information to patients/carers (89% versus 70%; P=0.024) and early discharge notification to general practitioners (80% versus 45%; P<0.001) were also more common in this group. There were no significant differences in the processes of interdisciplinary co-ordination and patient management between the integrated care pathways group and the control group. CONCLUSION: integrated care pathways may improve assessment and communication, even in specialist stroke settings.

Aged↗