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Rafael Contreras-Galindo,
Mark H Kaplan,
Shirley He,
Angie C Contreras-Galindo,
Marta J Gonzalez-Hernandez,
Ferdinand Kappes,
Derek Dube,
Susana M Chan,
Dan Robinson,
Fan Meng,
Manhong Dai, Scott D Gitlin,
Arul M Chinnaiyan,
Gilbert S Omenn,
David M Markovitz
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ABSTRACT: Human Endogenous Retroviruses (HERVs) make up 8% of the human genome. The HERV-K (HML-2) family is the most recent group of these viruses to have inserted into the genome, and we have detected the activation of HERV-K (HML-2) proviruses in the blood of patients with HIV-1 infection. We report that HIV-1 infection activates expression of a novel HERV-K (HML-2) provirus, termed K111, present in multiple copies in the centromeres of chromosomes throughout the human genome, yet not annotated in the most recent human genome assembly. Infection with HIV-1 or stimulation with the HIV-1 Tat protein leads to the activation of K111 proviruses. K111 is present as a single copy in the genome of the chimpanzee, yet K111 is not found in the genomes of other primates. Remarkably, K111 proviruses appear in the genomes of the extinct Neanderthal and Denisovan, while modern humans have at least 100 K111 proviruses spread across the centromeres of fifteen chromosomes. Our studies suggest that the progenitor K111 integrated before the Homo-Pan divergence and expanded in copy number during the evolution of hominins, perhaps by recombination. The expansion of K111 provides sequence evidence suggesting that recombination between the centromeres of various chromosomes took place during the evolution of humans. K111 proviruses show significant sequence variations in each individual centromere, which may serve as markers in future efforts to annotate human centromere sequences. Further, this work is an example of the potential to discover previously unknown genomic sequences through the analysis of nucleic acids found in the blood of patients.
Genome Research 05/2013; · 13.61 Impact Factor
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Rafael Contreras-Galindo,
Mark H Kaplan,
Angie C Contreras-Galindo,
Marta J Gonzalez-Hernandez,
Ilaria Ferlenghi,
Fabiola Giusti,
Eric Lorenzo, Scott D Gitlin,
Michael H Dosik,
Yasuhiro Yamamura,
David M Markovitz
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ABSTRACT: We previously reported finding the RNA of a type K human endogenous retrovirus, HERV-K (HML-2), at high titers in the plasma of HIV-1-infected and cancer patients (R. Contreras-Galindo et al., J. Virol. 82:9329-9236, 2008.). The extent to which the HERV-K (HML-2) proviruses become activated and the nature of their activated viral RNAs remain important questions. Therefore, we amplified and sequenced the full-length RNA of the env gene of the type 1 and 2 HERV-K (HML-2) viruses collected from the plasma of seven HIV-1-infected patients over a period of 1 to 3 years and from five breast cancer patients in order to reconstruct the genetic evolution of these viruses. HERV-K (HML-2) RNA was found in plasma fractions of HIV-1 patients at a density of ∼1.16 g/ml that contained both immature and correctly processed HERV-K (HML-2) proteins and virus-like particles that were recognized by anti-HERV-K (HML-2) antibodies. RNA sequences from novel HERV-K (HML-2) proviruses were discovered, including K111, which is specifically active during HIV-1 infection. Viral RNA arose from complete proviruses and proviruses devoid of a 5' long terminal repeat, suggesting that the expression of HERV-K (HML-2) RNA in these patients may involve sense and antisense transcription. In HIV-1-infected individuals, the HERV-K (HML-2) viral RNA showed evidence of frequent recombination, accumulation of synonymous rather than nonsynonymous mutations, and conserved N-glycosylation sites, suggesting that some of the HERV-K (HML-2) viral RNAs have undergone reverse transcription and are under purifying selection. In contrast, HERV-K (HML-2) RNA sequences found in the blood of breast cancer patients showed no evidence of recombination and exhibited only sporadic viral mutations. This study suggests that HERV-K (HML-2) is active in HIV-1-infected patients, and the resulting RNA message reveals previously undiscovered HERV-K (HML-2) genomic sequences.
Journal of Virology 01/2012; 86(1):262-76. · 5.40 Impact Factor
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Rafael Contreras-Galindo,
Mark H Kaplan,
Philippe Leissner,
Thibault Verjat,
Ilaria Ferlenghi,
Fabio Bagnoli,
Fabiola Giusti,
Michael H Dosik,
Daniel F Hayes, Scott D Gitlin,
David M Markovitz
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ABSTRACT: Actively replicating endogenous retroviruses entered the human genome millions of years ago and became a stable part of the inherited genetic material. They subsequently acquired multiple mutations, leading to the assumption that these viruses no longer replicate. However, certain human tumor cell lines have been shown to release endogenous retroviral particles. Here we show that RNA from human endogenous retrovirus K (HERV-K) (HML-2), a relatively recent entrant into the human genome, can be found in very high titers in the plasma of patients with lymphomas and breast cancer as measured by either reverse transcriptase PCR or nucleic acid sequence-based amplification. Further, these titers drop dramatically with cancer treatment. We also demonstrate the presence of reverse transcriptase and viral RNA in plasma fractions that contain both immature and correctly processed HERV-K (HML-2) Gag and envelope proteins. Finally, using immunoelectron microscopy, we show the presence of HERV-K (HML-2) virus-like particles in the plasma of lymphoma patients. Taken together, these findings demonstrate that elements of the endogenous retrovirus HERV-K (HML-2) can be found in the blood of modern-day humans with certain cancers.
Journal of Virology 10/2008; 82(19):9329-36. · 5.40 Impact Factor
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ABSTRACT: We wanted to identify what factors promote career development in patient-oriented clinical research (POCR).
We used a survey questionnaire covering areas relevant to the training of subspecialty fellows and the career development of POCR faculty.
Pursuit of an academic career after fellowship correlated with completion of a clinical project, availability of a clinical research training program, opportunity to earn academic credit, faculty mentorship, and obtaining independent career development funding. Successful faculty career development in POCR was closely correlated with excellent morale and adequate protected time for academic pursuits.
Specific academic environmental factors positively influence success in POCR hematology/oncology fellowship training and faculty career development.
Journal of Cancer Education 02/2005; 20(2):72-8. · 0.76 Impact Factor
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ABSTRACT: A survey of directors of adult and pediatric hematology/oncology subspecialty training programs in the United States and Canada was conducted to assess the environment in which recruitment and training is conducted in these medical disciplines. A total of 107 program directors responded to the survey, representing 66% of internal medicine and 47% of pediatric subspecialty programs in hematology or hematology/oncology. Specific areas covered in the web-based questionnaire included the type and demographics of the training program, profile of the training program director, characteristics of the applicant pool and existing trainee recruits, characteristics of the training program environment and curricula, research productivity of trainees, and the career pathways taken by recent training program graduates (including dominant areas of clinical interest). The results of this survey show considerable heterogeneity in the recruiting practices and the environment in which subspecialty training occurs, leading the authors to recommend improvements in or a heightened attention to issues, including recruitment of minority trainees, flexibility to recruit international medical school graduates, timing of trainee acceptance, maintaining the financial support of Medicare graduation medical education (GME), training of physician scientists, organization of the continuity clinic experience, visibility of nonmalignant hematology as a career path, and level of training program director support.
Blood 07/2004; 103(12):4383-8. · 9.90 Impact Factor
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Kaili Wu,
Maria Elena Bottazzi,
Cynthia de la Fuente,
Longwen Deng, Scott D Gitlin,
Anil Maddukuri,
Shabnam Dadgar,
Hong Li,
Akos Vertes,
Anne Pumfery,
Fatah Kashanchi
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ABSTRACT: Infection with human T-cell leukemia virus type 1 (HTLV-1) results in adult T-cell leukemia and HTLV-1-associated myelopathy/tropical spastic paraparesis. Tax, a 40-kDa protein, regulates viral and cellular transcription, host signal transduction, the cell cycle, and apoptosis. Tax has been shown to modulate cellular CREB and NFkappaB pathways; however, to date, its role in binding to various host cellular proteins involved in tumorigenesis has not been fully described. In this study, we describe the Tax-associated proteins and their functions in cells using several approaches. Tax eluted from a sizing column mostly at an apparent molecular mass of 1800 kDa. Following Tax immunoprecipitation, washes with high salt buffer, two-dimensional gel separation, and mass spectrometric analysis, a total of 32 proteins was identified. Many of these proteins belong to the signal transduction and cytoskeleton pathways and transcription/chromatin remodeling. A few of these proteins, including TXBP151, have been shown previously to bind to Tax. The interaction of Tax with small GTPase-cytoskeleton proteins, such as ras GAP1m, Rac1, Cdc42, RhoA, and gelsolin, indicates how Tax may regulate migration, invasion, and adhesion in T-cell cancers. Finally, the physical and functional association of Tax with the chromatin remodeling SWI/SNF complex was assessed using in vitro chromatin remodeling assays, chromatin remodeling factor BRG1 mutant cells, and RNA interference experiments. Collectively, Tax is able to bind and regulate many cellular proteins that regulate transcription and cytoskeletal related pathways, which might explain the pleiotropic effects of Tax leading to T-cell transformation and leukemia in HTLV-1-infected patients.
Journal of Biological Chemistry 02/2004; 279(1):495-508. · 4.77 Impact Factor
