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Procopio FA, Fromentin R, Kulpa DA, Brehm JH, Bebin AG, Strain MC, Richman DD, O'Doherty U, Palmer S, Hecht FM, Hoh R, Barnard RJO, Miller MD, Hazuda DJ, Deeks SG, Sékaly RP, Chomont N. A Novel Assay to Measure the Magnitude of the Inducible Viral Reservoir in HIV-infected Individuals. EBioMedicine 2015; 2:874-83. [PMID: 26425694 PMCID: PMC4563128 DOI: 10.1016/j.ebiom.2015.06.019] [Citation(s) in RCA: 217] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 06/23/2015] [Accepted: 06/23/2015] [Indexed: 12/19/2022] Open
Abstract
Background Quantifying latently infected cells is critical to evaluate the efficacy of therapeutic strategies aimed at reducing the size of the long-lived viral reservoir, but the low frequency of these cells makes this very challenging. Methods We developed TILDA (Tat/rev Induced Limiting Dilution Assay) to measure the frequency of cells with inducible multiply-spliced HIV RNA, as these transcripts are usually absent in latently infected cells but induced upon viral reactivation. TILDA requires less than a million cells, does not require RNA extraction and can be completed in two days. Findings In suppressed individuals on ART, we found the median frequency of latently infected CD4 + T cells as estimated by TILDA to be 24 cells/million, which was 48 times more than the frequency measured by the quantitative viral outgrowth assay, and 6–27 times less than the frequencies of cells harbouring viral DNA measured by PCR-based assays. TILDA measurements strongly correlated with most HIV DNA assays. The size of the latent reservoir measured by TILDA was lower in subjects who initiated ART during the early compared to late stage of infection (p = 0.011). In untreated HIV disease, the frequency of CD4 + cells carrying latent but inducible HIV largely exceeded the frequency of actively producing cells, demonstrating that the majority of infected cells are transcriptionally silent even in the absence of ART. Interpretations Our results suggest that TILDA is a reproducible and sensitive approach to measure the frequency of productively and latently infected cells in clinical settings. We demonstrate that the latent reservoir represents a substantial fraction of all infected cells prior to ART initiation. Research in context In this manuscript, we describe the development of a novel assay that measures the magnitude of the latent HIV reservoir, the main barrier to HIV eradication. This novel assay, termed TILDA for Tat/rev Induced Limiting Dilution Assay, requires only 10 ml of blood, does not necessitate extraction of viral nucleic acids, is highly reproducible, covers a wide dynamic range of reservoir sizes and can be completed in two days. As such, TILDA may represent an alternative to existing assays used to evaluate the efficacy of therapeutic strategies aimed at reducing the size of the latent HIV reservoir. We developed TILDA (Tat/rev Induced Limiting Dilution Assay) to measure the frequency of cells with inducible multiply-spliced HIV RNA in HIV-infected individuals on suppressive ART. Our results suggest that TILDA is a reproducible and sensitive approach to measure the frequency of productively and latently infected cells in clinical settings. Using TILDA, We demonstrate that the latent reservoir represents a substantial fraction of all infected cells prior to ART initiation.
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Affiliation(s)
| | - Rémi Fromentin
- Vaccine and Gene Therapy Institute Florida, Port St. Lucie, FL, USA
| | - Deanna A Kulpa
- Vaccine and Gene Therapy Institute Florida, Port St. Lucie, FL, USA
| | - Jessica H Brehm
- Vaccine and Gene Therapy Institute Florida, Port St. Lucie, FL, USA
| | | | - Matthew C Strain
- University of California San Diego, La Jolla, California and Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
| | - Douglas D Richman
- University of California San Diego, La Jolla, California and Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
| | - Una O'Doherty
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sarah Palmer
- Centre for Virus Research, Westmead Millennium Institute, Westmead, Australia ; Sydney Medical School, University of Sydney, Sydney, Australia
| | - Frederick M Hecht
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Rebecca Hoh
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | - Michael D Miller
- Infectious Disease, Merck Research Laboratories, West Point, PA, USA
| | - Daria J Hazuda
- Infectious Disease, Merck Research Laboratories, West Point, PA, USA
| | - Steven G Deeks
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | - Nicolas Chomont
- Vaccine and Gene Therapy Institute Florida, Port St. Lucie, FL, USA
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Rashid DJ, Chapman SC, Larsson HC, Organ CL, Bebin AG, Merzdorf CS, Bradley R, Horner JR. From dinosaurs to birds: a tail of evolution. EvoDevo 2014; 5:25. [PMID: 25621146 PMCID: PMC4304130 DOI: 10.1186/2041-9139-5-25] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 07/10/2014] [Indexed: 01/09/2023] Open
Abstract
A particularly critical event in avian evolution was the transition from long- to short-tailed birds. Primitive bird tails underwent significant alteration, most notably reduction of the number of caudal vertebrae and fusion of the distal caudal vertebrae into an ossified pygostyle. These changes, among others, occurred over a very short evolutionary interval, which brings into focus the underlying mechanisms behind those changes. Despite the wealth of studies delving into avian evolution, virtually nothing is understood about the genetic and developmental events responsible for the emergence of short, fused tails. In this review, we summarize the current understanding of the signaling pathways and morphological events that contribute to tail extension and termination and examine how mutations affecting the genes that control these pathways might influence the evolution of the avian tail. To generate a list of candidate genes that may have been modulated in the transition to short-tailed birds, we analyzed a comprehensive set of mouse mutants. Interestingly, a prevalent pleiotropic effect of mutations that cause fused caudal vertebral bodies (as in the pygostyles of birds) is tail truncation. We identified 23 mutations in this class, and these were primarily restricted to genes involved in axial extension. At least half of the mutations that cause short, fused tails lie in the Notch/Wnt pathway of somite boundary formation or differentiation, leading to changes in somite number or size. Several of the mutations also cause additional bone fusions in the trunk skeleton, reminiscent of those observed in primitive and modern birds. All of our findings were correlated to the fossil record. An open question is whether the relatively sudden appearance of short-tailed birds in the fossil record could be accounted for, at least in part, by the pleiotropic effects generated by a relatively small number of mutational events.
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Affiliation(s)
- Dana J Rashid
- Museum of the Rockies, Montana State University, 600 West Kagy Blvd, Bozeman, MT 59717, USA
| | - Susan C Chapman
- Department of Biological Sciences, Clemson University, 340 Long Hall, Clemson, SC 29634, USA
| | - Hans Ce Larsson
- Redpath Museum, McGill University, 859 Sherbrooke Street W., Montreal, Quebec H3A 0C4, Canada
| | - Chris L Organ
- Museum of the Rockies, Montana State University, 600 West Kagy Blvd, Bozeman, MT 59717, USA ; Department of Earth Sciences, Montana State University, 226 Traphagen Hall, Bozeman, MT 59717, USA
| | - Anne-Gaelle Bebin
- Museum of the Rockies, Montana State University, 600 West Kagy Blvd, Bozeman, MT 59717, USA ; Current address: Vaccine and Gene Therapy FL, 9801 Discovery Way, Port Lucie, FL 34987, USA
| | - Christa S Merzdorf
- Department of Cell Biology & Neuroscience, Montana State University, 513 Leon Johnson Hall, Bozeman, MT 59717, USA
| | - Roger Bradley
- Department of Cell Biology & Neuroscience, Montana State University, 513 Leon Johnson Hall, Bozeman, MT 59717, USA
| | - John R Horner
- Museum of the Rockies, Montana State University, 600 West Kagy Blvd, Bozeman, MT 59717, USA
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Habermann B, Bebin AG, Herklotz S, Volkmer M, Eckelt K, Pehlke K, Epperlein HH, Schackert HK, Wiebe G, Tanaka EM. An Ambystoma mexicanum EST sequencing project: analysis of 17,352 expressed sequence tags from embryonic and regenerating blastema cDNA libraries. Genome Biol 2004; 5:R67. [PMID: 15345051 PMCID: PMC522874 DOI: 10.1186/gb-2004-5-9-r67] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2003] [Revised: 05/06/2004] [Accepted: 06/29/2004] [Indexed: 11/30/2022] Open
Abstract
An EST database has been generated for the axolotl Ambystoma mexicanum. Analysis of this data has uncovered an unusual phylogenetic distribution of the cyclin dependent kinase inhibitor 1 gene family in amphibians. Background The ambystomatid salamander, Ambystoma mexicanum (axolotl), is an important model organism in evolutionary and regeneration research but relatively little sequence information has so far been available. This is a major limitation for molecular studies on caudate development, regeneration and evolution. To address this lack of sequence information we have generated an expressed sequence tag (EST) database for A. mexicanum. Results Two cDNA libraries, one made from stage 18-22 embryos and the other from day-6 regenerating tail blastemas, generated 17,352 sequences. From the sequenced ESTs, 6,377 contigs were assembled that probably represent 25% of the expressed genes in this organism. Sequence comparison revealed significant homology to entries in the NCBI non-redundant database. Further examination of this gene set revealed the presence of genes involved in important cell and developmental processes, including cell proliferation, cell differentiation and cell-cell communication. On the basis of these data, we have performed phylogenetic analysis of key cell-cycle regulators. Interestingly, while cell-cycle proteins such as the cyclin B family display expected evolutionary relationships, the cyclin-dependent kinase inhibitor 1 gene family shows an unusual evolutionary behavior among the amphibians. Conclusions Our analysis reveals the importance of a comprehensive sequence set from a representative of the Caudata and illustrates that the EST sequence database is a rich source of molecular, developmental and regeneration studies. To aid in data mining, the ESTs have been organized into an easily searchable database that is freely available online.
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Affiliation(s)
- Bianca Habermann
- Scionics Computer Innovation GmbH, Pfotenhauerstrasse 110, Dresden 01307, Germany
| | - Anne-Gaelle Bebin
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, Dresden 01307, Germany
| | - Stephan Herklotz
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, Dresden 01307, Germany
| | - Michael Volkmer
- Scionics Computer Innovation GmbH, Pfotenhauerstrasse 110, Dresden 01307, Germany
| | - Kay Eckelt
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, Dresden 01307, Germany
| | - Kerstin Pehlke
- Institute of Anatomy, Medical Faculty of the Carl Gustav Carus Technical University, Dresden, Fetscherstrasse 74, Dresden 01307, Germany
| | - Hans Henning Epperlein
- Institute of Anatomy, Medical Faculty of the Carl Gustav Carus Technical University, Dresden, Fetscherstrasse 74, Dresden 01307, Germany
| | - Hans Konrad Schackert
- Department of Surgical Research, Medical Faculty of the Carl Gustav Carus Technical University, Dresden, Fetscherstrasse 74, Dresden 01307, Germany
| | - Glenis Wiebe
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, Dresden 01307, Germany
| | - Elly M Tanaka
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, Dresden 01307, Germany
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