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Szeto MD, Maymone MBC, Presley CL, Laughter MR, Lada SM, Runion TM, Barber C, Fonseca AS, Dellavalle RP. Citation indicators revisited: Reply to Top Authors in Dermatology. J Am Acad Dermatol 2022; 87:1408-1410. [PMID: 36075280 DOI: 10.1016/j.jaad.2022.08.054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 11/18/2022]
Affiliation(s)
- Mindy D Szeto
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Mayra B C Maymone
- Department of Dermatology, Brown University, Providence, Rhode Island
| | - Colby L Presley
- Division of Dermatology, Lehigh Valley Health Network, Allentown, Pennsylvania
| | - Melissa R Laughter
- The Ronald O. Perelman Department of Dermatology, New York University School of Medicine, New York, New York
| | - Steven M Lada
- Department of Emergency Medicine, UHS SoCal MEC, Temecula, California
| | - Taylor M Runion
- Rocky Vista University College of Osteopathic Medicine, Parker, Colorado
| | - Cara Barber
- Department of Dermatology, Good Samaritan Regional Medical Center/Silver Falls Dermatology, Salem, Oregon
| | - Allene S Fonseca
- Department of Dermatology, Wayne State University, Detroit, Michigan
| | - Robert P Dellavalle
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, Colorado.
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2
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Szeto MD, Presley CL, Maymone MBC, Laughter MR, Lada SM, Runion TM, Barber C, Fonseca A, Dellavalle RP. Top authors in dermatology by h-index: A bibliometric analysis of 1980-2020. J Am Acad Dermatol 2021; 85:1573-1579. [PMID: 33217507 DOI: 10.1016/j.jaad.2020.10.087] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/23/2020] [Accepted: 10/27/2020] [Indexed: 11/24/2022]
Affiliation(s)
- Mindy D Szeto
- School of Medicine, University of Colorado, Aurora, CO
| | - Colby L Presley
- College of Osteopathic Medicine, Rocky Vista University, Parker, CO
| | - Mayra B C Maymone
- Department of Surgery, University of Colorado Anschutz Medical Campus, Aurora, CO
| | | | - Steven M Lada
- School of Medicine, University of Colorado, Aurora, CO
| | - Taylor M Runion
- College of Osteopathic Medicine, Rocky Vista University, Parker, CO
| | - Cara Barber
- Department of Medicine, University of California, San Diego, CA
| | - Allene Fonseca
- Department of Medicine, Division of Dermatology, University of Washington, Seattle, WA
| | - Robert P Dellavalle
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, CO; Dermatology Service, US Department of Veterans Affairs Rocky Mountain Regional Medical Center, Aurora, CO.
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3
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Papasavvas E, Azzoni L, Ross BN, Fair M, Yuan Z, Gyampoh K, Mackiewicz A, Sciorillo AC, Pagliuzza A, Lada SM, Wu G, Goh SL, Bahnck-Teets C, Holder DJ, Zuck PD, Damra M, Lynn KM, Tebas P, Mounzer K, Kostman JR, Abdel-Mohsen M, Richman D, Chomont N, Howell BJ, Montaner LJ. Intact Human Immunodeficiency Virus (HIV) Reservoir Estimated by the Intact Proviral DNA Assay Correlates With Levels of Total and Integrated DNA in the Blood During Suppressive Antiretroviral Therapy. Clin Infect Dis 2021; 72:495-498. [PMID: 33527127 DOI: 10.1093/cid/ciaa809] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/12/2020] [Indexed: 02/06/2023] Open
Abstract
Accurate characterization of the human immunodeficiency virus (HIV) reservoir is imperative to develop an effective cure. HIV was measured in antiretroviral therapy-suppressed individuals using the intact proviral DNA assay (IPDA), along with assays for total or integrated HIV DNA, and inducible HIV RNA or p24. Intact provirus correlated with total and integrated HIV.
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Affiliation(s)
| | - Livio Azzoni
- Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Brian N Ross
- Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Matthew Fair
- Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Zhe Yuan
- Wistar Institute, Philadelphia, Pennsylvania, USA
| | | | | | | | | | - Steven M Lada
- Veterans Affairs San Diego Healthcare System and the University of California, San Diego, California, USA
| | - Guoxin Wu
- Merck & Co., Inc., Kenilworth, New Jersey, USA
| | | | | | | | - Paul D Zuck
- Merck & Co., Inc., Kenilworth, New Jersey, USA
| | | | - Kenneth M Lynn
- Presbyterian Hospital, University of Pennsylvania hospital, Philadelphia, Pennsylvania, USA
| | - Pablo Tebas
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Karam Mounzer
- Jonathan Lax Immune Disorders Treatment Center, Philadelphia Field Initiating Group for HIV-1 Trials, Philadelphia, Pennsylvania, USA
| | - Jay R Kostman
- John Bell Health Center, Philadelphia Field Initiating Group for HIV-1 Trials, Philadelphia, Pennsylvania, USA
| | | | - Douglas Richman
- Veterans Affairs San Diego Healthcare System and the University of California, San Diego, California, USA
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4
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Szeto MD, Sivesind TE, Presley CL, Harp T, Meckley AL, Afrin A, Lada SM, Laughter MR, Maymone MBC, Dellavalle RP. Top authors in dermatology: Comparisons of standardized database citation indicators. J Am Acad Dermatol 2021; 85:e57-e59. [PMID: 33774089 DOI: 10.1016/j.jaad.2021.03.068] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/13/2021] [Accepted: 03/18/2021] [Indexed: 11/27/2022]
Affiliation(s)
- Mindy D Szeto
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Torunn E Sivesind
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Colby L Presley
- College of Osteopathic Medicine, Rocky Vista University, Parker, Colorado
| | - Taylor Harp
- College of Osteopathic Medicine, Rocky Vista University, Parker, Colorado
| | - Abigail L Meckley
- College of Osteopathic Medicine, Rocky Vista University, Parker, Colorado
| | - Antara Afrin
- College of Human Medicine, Michigan State University, East Lansing, Michigan
| | - Steven M Lada
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Melissa R Laughter
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Mayra B C Maymone
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Robert P Dellavalle
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, Colorado; Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, Colorado.
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5
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Presley CL, Florek AG, Ricotti CM, Rundle CW, Husayn SS, Szeto MD, Rietcheck HR, Lada SM, Militello M, Pulsipher KJ, Olayinka JT, Dellavalle RP. A Clinical Impact Score: a novel and clinically significant measure of journal influence. Dermatol Online J 2020; 26:13030/qt9z47f8r8. [PMID: 33423431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 12/29/2020] [Indexed: 06/12/2023] Open
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Robert P Dellavalle
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, CO Dermatology Service, US Department of Veterans Affairs Rocky Mountain Regional Medical Center, Aurora, CO.
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6
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Szeto MD, Lada SM, Husayn SS, Presley CL, Militello M, Dellavalle RP. A survey of article types in the dermatology literature. J Am Acad Dermatol 2020; 84:1439-1441. [PMID: 32590032 DOI: 10.1016/j.jaad.2020.06.084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 06/17/2020] [Indexed: 11/25/2022]
Affiliation(s)
- Mindy D Szeto
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Steven M Lada
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Sameeha S Husayn
- College of Osteopathic Medicine, Rocky Vista University, Parker, Colorado
| | - Colby L Presley
- College of Osteopathic Medicine, Rocky Vista University, Parker, Colorado
| | - Michelle Militello
- College of Osteopathic Medicine, Rocky Vista University, Parker, Colorado
| | - Robert P Dellavalle
- Department of Dermatology, University of Colorado School of Medicine, Aurora, Colorado; Dermatology Service, Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, Colorado.
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Presley CL, Florek AG, Ricotti CM, Rundle CW, Husayn SS, Szeto MD, Rietcheck HR, Lada SM, Militello M, Pulsipher KJ, Olayinka JT, Dellavalle RP. A Clinical Impact Score: a novel and clinically significant measure of journal influence. Dermatol Online J 2020. [DOI: 10.5070/d32612051367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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8
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Richman DD, Huang K, Lada SM, Sun X, Jain S, Massanella M, Menke B. Replication competence of virions induced from CD4+ lymphocytes latently infected with HIV. Retrovirology 2019; 16:4. [PMID: 30770748 PMCID: PMC6377736 DOI: 10.1186/s12977-019-0466-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 02/06/2019] [Indexed: 11/16/2022] Open
Abstract
Latently infected CD4 lymphocytes preclude cure of HIV infection, even with the most effective antiretroviral therapy. The replication competent latent HIV reservoir has been quantified with the terminal dilution quantitative viral outgrowth assay, which induces virus propagation in CD4+ T cell culture supernatants following cellular activation. Efforts to improve the sensitivity of this inefficient assay have introduced more sensitive p24 ELISA and RNA PCR based endpoints, but these more sensitive endpoints have raised the question whether they are measuring induced replication competent or defective virions. Here we performed parallel terminal dilution assays with CD4 lymphocytes from subjects effectively treated with antiretroviral therapy. An HIV integrase inhibitor was incorporated into one set of parallel cultures to compare the frequency of cells that can be induced to produce virions to those that produce virus that can propagate and amplify with co-culture in permissive cells. The majority of cells that can be induced to generate virus particles are producing replication competent virus, thus justifying more sensitive and faster assays of this reservoir.
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Affiliation(s)
- Douglas D. Richman
- San Diego Veterans Affairs Healthcare System, San Diego, CA USA
- University of California San Diego, La Jolla, CA USA
| | - Karissa Huang
- San Diego Veterans Affairs Healthcare System, San Diego, CA USA
- Present Address: University of California, Irvine, CA USA
| | - Steven M. Lada
- San Diego Veterans Affairs Healthcare System, San Diego, CA USA
- Present Address: University of Colorado Denver School of Medicine, Aurora, CO USA
| | - Xiaoying Sun
- University of California San Diego, La Jolla, CA USA
| | - Sonia Jain
- University of California San Diego, La Jolla, CA USA
| | | | - Bryson Menke
- San Diego Veterans Affairs Healthcare System, San Diego, CA USA
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9
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Massanella M, Yek C, Lada SM, Nakazawa M, Shefa N, Huang K, Richman DD. Improved assays to measure and characterize the inducible HIV reservoir. EBioMedicine 2018; 36:113-121. [PMID: 30316868 PMCID: PMC6197429 DOI: 10.1016/j.ebiom.2018.09.036] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [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: 07/03/2018] [Revised: 09/16/2018] [Accepted: 09/19/2018] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Improved assays are critical to better characterize the HIV reservoir and to reliably evaluate candidate intervention strategies. Here we describe different methods to quantify the HIV reservoir. METHODS We developed an optimized quantitative viral outgrowth assay (QVOA) to quantify the frequency of cells harboring replication-competent HIV, which is simpler and more sensitive than classical QVOAs. We also developed new inducible RNA assays that concomitantly measure the frequency of cell-associated [ca-] (gag and tat-rev) and cell-free [cf-] HIV RNA after three days of anti-CD3/CD28 stimulation. FINDINGS The median frequency of the infected cells measured after induction was 94 IQR[60-132], 16 IQR [9-29] and 2.9 IQR[1.9-6.8] cells/106 CD4+ T-cells for ca-RNA gag and tat-rev, and cf-RNA, respectively. There are a large proportion of transcription-competent proviruses (ca-RNA) that seemed unable to form complete virions (cf-RNA), suggesting post-transcriptional blocks or defective proviruses. Importantly, the median frequency of infected CD4+ T-cells as estimated by 3-day inducible cf-RNA assay was not statistically different from the frequency measured by the QVOA (median of 3.3 [1.9-6.2] IUPM). The latently infected cells detected by the inducible cf-RNA assay correlated highly with the QVOA ( r= 0.67, p < .001), and both assays were equivalent in 60% of the samples tested, suggesting that most cells induced to produce virions are generating replication-competent virus. INTERPRETATION These inducible RNA assays provide more sensitivity and a greater dynamic range for the monitoring of reduction of the reservoir by eradication strategies. Such assays may serve as robust and useful tools for clinical investigations of the HIV reservoir.
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Affiliation(s)
| | - Christina Yek
- University of California San Diego, La Jolla, CA, USA
| | - Steven M Lada
- University of California San Diego, La Jolla, CA, USA
| | | | - Neda Shefa
- University of California San Diego, La Jolla, CA, USA
| | - Karissa Huang
- University of California San Diego, La Jolla, CA, USA
| | - Douglas D Richman
- University of California San Diego, La Jolla, CA, USA; Veterans Affairs San Diego Healthcare System, La Jolla, CA, USA.
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10
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White CH, Beliakova-Bethell N, Lada SM, Breen MS, Hurst TP, Spina CA, Richman DD, Frater J, Magiorkinis G, Woelk CH. Transcriptional Modulation of Human Endogenous Retroviruses in Primary CD4+ T Cells Following Vorinostat Treatment. Front Immunol 2018; 9:603. [PMID: 29706951 PMCID: PMC5906534 DOI: 10.3389/fimmu.2018.00603] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 03/09/2018] [Indexed: 12/19/2022] Open
Abstract
The greatest obstacle to a cure for HIV is the provirus that integrates into the genome of the infected cell and persists despite antiretroviral therapy. A "shock and kill" approach has been proposed as a strategy for an HIV cure whereby drugs and compounds referred to as latency-reversing agents (LRAs) are used to "shock" the silent provirus into active replication to permit "killing" by virus-induced pathology or immune recognition. The LRA most utilized to date in clinical trials has been the histone deacetylase (HDAC) inhibitor-vorinostat. Potentially, pathological off-target effects of vorinostat may result from the activation of human endogenous retroviruses (HERVs), which share common ancestry with exogenous retroviruses including HIV. To explore the effects of HDAC inhibition on HERV transcription, an unbiased pharmacogenomics approach (total RNA-Seq) was used to evaluate HERV expression following the exposure of primary CD4+ T cells to a high dose of vorinostat. Over 2,000 individual HERV elements were found to be significantly modulated by vorinostat, whereby elements belonging to the ERVL family (e.g., LTR16C and LTR33) were predominantly downregulated, in contrast to LTR12 elements of the HERV-9 family, which exhibited the greatest signal, with the upregulation of 140 distinct elements. The modulation of three different LTR12 elements by vorinostat was confirmed by droplet digital PCR along a dose-response curve. The monitoring of LTR12 expression during clinical trials with vorinostat may be indicated to assess the impact of this HERV on the human genome and host immunity.
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Affiliation(s)
- Cory H. White
- Faculty of Medicine, University of Southampton, Southampton, Hants, United Kingdom
| | - Nadejda Beliakova-Bethell
- San Diego VA Medical Center and Veterans Medical Research Foundation, San Diego, CA, United States
- Department of Medicine, University of California San Diego, La Jolla, CA, United States
| | - Steven M. Lada
- San Diego VA Medical Center and Veterans Medical Research Foundation, San Diego, CA, United States
| | - Michael S. Breen
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Tara P. Hurst
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Celsa A. Spina
- San Diego VA Medical Center and Veterans Medical Research Foundation, San Diego, CA, United States
- Department of Pathology, University of California San Diego, La Jolla, CA, United States
| | - Douglas D. Richman
- San Diego VA Medical Center and Veterans Medical Research Foundation, San Diego, CA, United States
- Department of Medicine, University of California San Diego, La Jolla, CA, United States
- Department of Pathology, University of California San Diego, La Jolla, CA, United States
| | - John Frater
- Nuffield Department of Clinical Medicine, Peter Medawar Building for Pathogen Research, South Parks Road, Oxford, United Kingdom
| | | | - Christopher H. Woelk
- Faculty of Medicine, University of Southampton, Southampton, Hants, United Kingdom
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Cummins NW, Rizza S, Litzow MR, Hua S, Lee GQ, Einkauf K, Chun TW, Rhame F, Baker JV, Busch MP, Chomont N, Dean PG, Fromentin R, Haase AT, Hampton D, Keating SM, Lada SM, Lee TH, Natesampillai S, Richman DD, Schacker TW, Wietgrefe S, Yu XG, Yao JD, Zeuli J, Lichterfeld M, Badley AD. Extensive virologic and immunologic characterization in an HIV-infected individual following allogeneic stem cell transplant and analytic cessation of antiretroviral therapy: A case study. PLoS Med 2017; 14:e1002461. [PMID: 29182633 PMCID: PMC5705162 DOI: 10.1371/journal.pmed.1002461] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 10/25/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Notwithstanding 1 documented case of HIV-1 cure following allogeneic stem cell transplantation (allo-SCT), several subsequent cases of allo-SCT in HIV-1 positive individuals have failed to cure HIV-1 infection. The aim of our study was to describe changes in the HIV reservoir in a single chronically HIV-infected patient on suppressive antiretroviral therapy who underwent allo-SCT for treatment of acute lymphoblastic leukemia. METHODS AND FINDINGS We prospectively collected peripheral blood mononuclear cells (PBMCs) by leukapheresis from a 55-year-old man with chronic HIV infection before and after allo-SCT to measure the size of the HIV-1 reservoir and characterize viral phylogeny and phenotypic changes in immune cells. At day 784 post-transplant, when HIV-1 was undetectable by multiple measures-including PCR measurements of both total and integrated HIV-1 DNA, replication-competent virus measurement by large cell input quantitative viral outgrowth assay, and in situ hybridization of colon tissue-the patient consented to an analytic treatment interruption (ATI) with frequent clinical monitoring. He remained aviremic off antiretroviral therapy until ATI day 288, when a low-level virus rebound of 60 HIV-1 copies/ml occurred, which increased to 1,640 HIV-1 copies/ml 5 days later, prompting reinitiation of ART. Rebounding plasma HIV-1 sequences were phylogenetically distinct from proviral HIV-1 DNA detected in circulating PBMCs before transplantation. The main limitations of this study are the insensitivity of reservoir measurements, and the fact that it describes a single case. CONCLUSIONS allo-SCT led to a significant reduction in the size of the HIV-1 reservoir and a >9-month-long ART-free remission from HIV-1 replication. Phylogenetic analyses suggest that the origin of rebound virus was distinct from the viruses identified pre-transplant in the PBMCs.
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Affiliation(s)
- Nathan W. Cummins
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Stacey Rizza
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Mark R. Litzow
- Division of Hematology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Stephane Hua
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Guinevere Q. Lee
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Kevin Einkauf
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Tae-Wook Chun
- HIV Immunovirology Unit, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Frank Rhame
- Abbott Northwestern Hospital, Allina Health, Minneapolis, Minnesota, United States of America
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Jason V. Baker
- Division of Infectious Diseases, Hennepin County Medical Center, Minneapolis, Minnesota, United States of America
| | - Michael P. Busch
- Blood Systems Research Institute, San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Nicolas Chomont
- Centre de Recherche du CHUM, University of Montreal Hospital Centre, Montreal, Canada
- Department of Microbiology, Infectious Diseases and Immunology, University of Montreal, Montreal, Canada
| | - Patrick G. Dean
- Division of Transplantation Surgery, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Rémi Fromentin
- Centre de Recherche du CHUM, University of Montreal Hospital Centre, Montreal, Canada
- Department of Microbiology, Infectious Diseases and Immunology, University of Montreal, Montreal, Canada
| | - Ashley T. Haase
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Dylan Hampton
- Blood Systems Research Institute, San Francisco, California, United States of America
| | - Sheila M. Keating
- Blood Systems Research Institute, San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Steven M. Lada
- University of California, San Diego, San Diego, California, United States of America
- VA San Diego Healthcare System, San Diego, California, United States of America
| | - Tzong-Hae Lee
- Blood Systems Research Institute, San Francisco, California, United States of America
| | - Sekar Natesampillai
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Douglas D. Richman
- University of California, San Diego, San Diego, California, United States of America
- VA San Diego Healthcare System, San Diego, California, United States of America
| | - Timothy W. Schacker
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Stephen Wietgrefe
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Xu G. Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Joseph D. Yao
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - John Zeuli
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Andrew D. Badley
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, United States of America
- * E-mail:
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12
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Massanella M, Gianella S, Lada SM, Richman DD, Strain MC. Quantification of Total and 2-LTR (Long terminal repeat) HIV DNA, HIV RNA and Herpesvirus DNA in PBMCs. Bio Protoc 2015; 5:e1492. [PMID: 27478862 DOI: 10.21769/bioprotoc.1492] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Almost all individuals infected with human immunodeficiency virus (HIV) are also infected with cytomegalovirus (CMV) and Epstein Barr virus (EBV). The aims of our studies have included characterizing and measuring the latent HIV reservoir and understanding the association between asymptomatic replication of CMV (and other herpesvirus, including EBV) and this HIV reservoir (Gianella et al., 2014). This protocol was designed to simultaneously co-extract DNA and RNA from the same peripheral blood mononuclear cell (PBMC) aliquot and quantify HIV, CMV and EBV DNA, as well as HIV RNA using droplet digital PCR (ddPCR). For collection and processing of male genital secretions and quantification of HIV RNA and DNA from seven human herpesviruses from seminal plasma, refer to protocol "Quantification of HIV RNA and Human Herpesvirus DNA in Seminal Plasma" (Vargas-Meneses et al., 2015).
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Affiliation(s)
| | | | | | - Douglas D Richman
- University of California San Diego, La Jolla, USA; Veterans Affairs San Diego Healthcare System, La Jolla, USA
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13
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Wang C, Abdel-Mohsen M, Strain MC, Lada SM, Yukl S, Cockerham LR, Pilcher CD, Hecht FM, Sinclair E, Liegler T, Richman DD, Deeks SG, Pillai SK. Decreased HIV type 1 transcription in CCR5-Δ32 heterozygotes during suppressive antiretroviral therapy. J Infect Dis 2014; 210:1838-43. [PMID: 24935955 DOI: 10.1093/infdis/jiu338] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Individuals who are heterozygous for the CCR5-Δ32 mutation provide a natural model to examine the effects of reduced CCR5 expression on human immunodeficiency virus (HIV) persistence. We evaluated the HIV reservoir in 18 CCR5-Δ32 heterozygotes and 54 CCR5 wild-type individuals during suppressive antiretroviral therapy. Cell-associated HIV RNA levels (P=.035), RNA to DNA transcriptional ratios (P=.013), and frequency of detectable HIV 2-long terminal repeat circular DNA (P=.013) were significantly lower in CD4+ T cells from CCR5-Δ32 heterozygotes. Cell-associated HIV RNA was significantly correlated with CCR5 surface expression on CD4+ T cells (r2=0.136; P=.002). Our findings suggest that curative strategies should further explore manipulation of CCR5.
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Affiliation(s)
- Charlene Wang
- Emory University, Atlanta, Georgia Blood Systems Research Institute
| | | | - Matthew C Strain
- University of California-San Diego Veterans Affairs San Diego Healthcare System, California
| | - Steven M Lada
- University of California-San Diego Veterans Affairs San Diego Healthcare System, California
| | - Steven Yukl
- University of California-San Francisco San Francisco Veterans Affairs Medical Center
| | | | | | | | | | | | - Douglas D Richman
- University of California-San Diego Veterans Affairs San Diego Healthcare System, California
| | | | - Satish K Pillai
- Blood Systems Research Institute University of California-San Francisco
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14
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Massanella M, Singhania A, Beliakova-Bethell N, Pier R, Lada SM, White CH, Pérez-Santiago J, Blanco J, Richman DD, Little SJ, Woelk CH. Differential gene expression in HIV-infected individuals following ART. Antiviral Res 2013; 100:420-8. [PMID: 23933117 DOI: 10.1016/j.antiviral.2013.07.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 07/23/2013] [Accepted: 07/25/2013] [Indexed: 01/13/2023]
Abstract
Previous studies of the effect of ART on gene expression in HIV-infected individuals have identified small numbers of modulated genes. Since these studies were underpowered or cross-sectional in design, a paired analysis of peripheral blood mononuclear cells (PBMCs), isolated before and after ART, from a robust number of HIV-infected patients (N=32) was performed. Gene expression was assayed by microarray and 4157 differentially expressed genes (DEGs) were identified following ART using multivariate permutation tests. Pathways and gene ontology (GO) terms over-represented for DEGs reflected the transition from a period of active virus replication before ART to one of viral suppression (e.g., repression of JAK-STAT signaling) and possible prolonged drug exposure (e.g., oxidative phosphorylation pathway) following ART. CMYC was the DEG whose product made the greatest number of interactions at the protein level in protein interaction networks (PINs), which has implications for the increased incidence of Hodgkin's lymphoma (HL) in HIV-infected patients. The differential expression of multiple genes was confirmed by RT-qPCR including well-known drug metabolism genes (e.g., ALOX12 and CYP2S1). Targets not confirmed by RT-qPCR (i.e., GSTM2 and RPL5) were significantly confirmed by droplet digital (ddPCR), which may represent a superior method when confirming DEGs with low fold changes. In conclusion, a paired design revealed that the number of genes modulated following ART was an order of magnitude higher than previously recognized.
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Affiliation(s)
- Marta Massanella
- Fundació irsiCaixa-HIVACAT, Institut de Recerca en Ciències de la Salut Germans Trias i Pujol (IGTP), Hospital Germans Trias, Universitat Autònoma de Barcelona, 08916 Badalona, Spain; Veterans Affairs San Diego Healthcare System, San Diego, CA 92161, USA; Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
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15
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Perry ST, Buck MD, Plummer EM, Penmasta RA, Batra H, Stavale EJ, Warfield KL, Dwek RA, Butters TD, Alonzi DS, Lada SM, King K, Klose B, Ramstedt U, Shresta S. An iminosugar with potent inhibition of dengue virus infection in vivo. Antiviral Res 2013; 98:35-43. [DOI: 10.1016/j.antiviral.2013.01.004] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 01/16/2013] [Accepted: 01/22/2013] [Indexed: 11/26/2022]
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16
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Prestwood TR, Morar MM, Zellweger RM, Miller R, May MM, Yauch LE, Lada SM, Shresta S. Gamma interferon (IFN-γ) receptor restricts systemic dengue virus replication and prevents paralysis in IFN-α/β receptor-deficient mice. J Virol 2012; 86:12561-70. [PMID: 22973027 PMCID: PMC3497655 DOI: 10.1128/jvi.06743-11] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Accepted: 08/27/2012] [Indexed: 02/03/2023] Open
Abstract
We previously reported that mice lacking alpha/beta and gamma interferon receptors (IFN-α/βR and -γR) uniformly exhibit paralysis following infection with the dengue virus (DENV) clinical isolate PL046, while only a subset of mice lacking the IFN-γR alone and virtually no mice lacking the IFN-α/βR alone develop paralysis. Here, using a mouse-passaged variant of PL046, strain S221, we show that in the absence of the IFN-α/βR, signaling through the IFN-γR confers approximately 140-fold greater resistance against systemic vascular leakage-associated dengue disease and virtually complete protection from dengue-induced paralysis. Viral replication in the spleen was assessed by immunohistochemistry and flow cytometry, which revealed a reduction in the number of infected cells due to IFN-γR signaling by 2 days after infection, coincident with elevated levels of IFN-γ in the spleen and serum. By 4 days after infection, IFN-γR signaling was found to restrict DENV replication systemically. Clearance of DENV, on the other hand, occurred in the absence of IFN-γR, except in the central nervous system (CNS) (brain and spinal cord), where clearance relied on IFN-γ from CD8(+) T cells. These results demonstrate the roles of IFN-γR signaling in protection from initial systemic and subsequent CNS disease following DENV infection and demonstrate the importance of CD8(+) T cells in preventing DENV-induced CNS disease.
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Affiliation(s)
- Tyler R Prestwood
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
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17
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Perry ST, Buck MD, Lada SM, Schindler C, Shresta S. STAT2 mediates innate immunity to Dengue virus in the absence of STAT1 via the type I interferon receptor. PLoS Pathog 2011; 7:e1001297. [PMID: 21379341 PMCID: PMC3040673 DOI: 10.1371/journal.ppat.1001297] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Accepted: 01/18/2011] [Indexed: 12/23/2022] Open
Abstract
Dengue virus (DENV) is a mosquito-borne flavivirus, and symptoms of infection range from asymptomatic to the severe dengue hemorrhagic fever/dengue shock syndrome (DHF/DSS). High viral loads correlate with disease severity, and both type I & II interferons (IFNs) are crucial for controlling viral replication. We have previously reported that signal transducer and activator of transcription (STAT) 1-deficient mice are resistant to DENV-induced disease, but little is known about this STAT1-independent mechanism of protection. To determine the molecular basis of the STAT1-independent pathway, mice lacking STAT1, STAT2, or both STAT1 and STAT2 were infected with a virulent mouse-adapted strain of DENV2. In the first 72 hours of infection, the single-deficient mice lacking STAT1 or STAT2 possessed 50–100 fold higher levels of viral RNA than wild type mice in the serum, spleen, and other visceral tissues, but remained resistant to DENV-induced death. In contrast, the double-deficient mice exhibited the early death phenotype previously observed in type I and II IFN receptor knockout mice (AG129), indicating that STAT2 is the mediator of the STAT1-independent host defense mechanism. Further studies demonstrated that this STAT2-dependent STAT1-independent mechanism requires the type I IFN receptor, and contributes to the autocrine amplification of type I IFN expression. Examination of gene expression in the spleen and bone marrow-derived macrophages following DENV infection revealed STAT2-dependent pathways can induce the transcription of a subset of interferon stimulated genes even in the absence of STAT1. Collectively, these results help elucidate the nature of the poorly understood STAT1-independent host defense mechanism against viruses by identifying a functional type I IFN/STAT2 signaling pathway following DENV infection in vivo. Dengue virus (DENV) is a mosquito-borne pathogen present in the tropical and sub-tropical regions of the world, and an estimated 2.5 billion people are at risk of infection. Interferon (IFN) mediated innate responses in the host are critical for limiting viral spread following DENV infection. We have previously demonstrated that mice lacking STAT1, a key mediator of both type I and II IFN responses, are not susceptible to DENV-mediated disease. In this study, we sought to determine the mechanism responsible for protection against DENV disease in the absence of STAT1. Using knockout mice, we identify STAT2 as the protein that mediates type I IFN signaling during DENV infection in the absence of STAT1. The resulting antiviral response includes amplification of type I IFN and the expression of interferon stimulated genes. These data suggest DENV infection is especially sensitive to STAT2-mediated antiviral responses in vivo, and provide novel insights towards how IFNs protect against viral infections.
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Affiliation(s)
- Stuart T. Perry
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America
| | - Michael D. Buck
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America
| | - Steven M. Lada
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America
| | - Christian Schindler
- Department of Microbiology and Immunology, Columbia University, New York, New York, United States of America
| | - Sujan Shresta
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America
- * E-mail:
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