Evidence map›Paper›PMID 27875997›Full record

ArticleBMC infectious diseases2016

Identification of the transcripts associated with spontaneous HCV clearance in individuals co-infected with HIV and HCV.

Yue Chen, Chengli Shen, Debjani Guha, Ming Ding, Scott Kulich, Aiymkul Ashimkhanova, Charles Rinaldo, Eric Seaberg, Joseph B Margolick, Valentina Stosor and 2 more

Open access · goldAbstract readMulticenter Study
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC infectious diseases, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
0.4field-weighted citation impact, top 33% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed, 3 citations in OpenAlex.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

12 authors at 4 institutions in 1 country.

Yue ChenDepartment of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, 2138 Parran Hall, 130 DeSoto Street, Pittsburgh, Pa, 15261, USA. cheny@pitt.edu.
Chengli ShenDepartment of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, 2138 Parran Hall, 130 DeSoto Street, Pittsburgh, Pa, 15261, USA.
Debjani GuhaDepartment of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, 2138 Parran Hall, 130 DeSoto Street, Pittsburgh, Pa, 15261, USA.
Ming DingDepartment of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, 2138 Parran Hall, 130 DeSoto Street, Pittsburgh, Pa, 15261, USA.
Scott KulichDepartment of Pathology, VA Hospital, Pittsburgh, Pa, USA.
Aiymkul AshimkhanovaDepartment of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, 2138 Parran Hall, 130 DeSoto Street, Pittsburgh, Pa, 15261, USA.
Charles RinaldoDepartment of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, 2138 Parran Hall, 130 DeSoto Street, Pittsburgh, Pa, 15261, USA.
Eric SeabergDepartment of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.
Joseph B MargolickDepartment of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.
Valentina StosorDivision of Infectious Diseases, School of Medicine, Northwestern University, Chicago, IL, USA.
Otoniel Martínez-MazaDepartment of Epidemiology, UCLA Fielding School of Public Health, and Departments of Obstetrics & Gynecology and Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.
Phalguni GuptaDepartment of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, 2138 Parran Hall, 130 DeSoto Street, Pittsburgh, Pa, 15261, USA.
University of Pittsburgh · USJohns Hopkins University · USNorthwestern University · USUniversity of California, Los Angeles · US

Funding

Institute for Clinical and Translational Research (UL1)UL1RR025005 · NCRR · JOHNS HOPKINS UNIVERSITY · PI FORD, DANIEL ERNEST · 2007 to 2011
$75.8M
NATURAL HISTORY OF AIDS IN HOMOSEXUAL MENU01AI035040 · NIAID · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI DETELS, ROGER, MARTINEZ-MAZA, OTONIEL · 1993 to 2018
$75.2M
University of Pittsburgh Multicenter AIDS Cohort Study (MACS)U01AI035041 · NIAID · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI MARTINSON, JEREMY JAMES, RINALDO, CHARLES R · 1993 to 2018
$71.4M
MULTICENTER AIDS COHORT STUDYU01AI035039 · NIAID · NORTHWESTERN UNIVERSITY AT CHICAGO · PI WOLINSKY, STEVEN M · 1993 to 2018
$66.4M
Multicenter Aids Cohort Study- Part B (Baltimore Site)U01AI035042 · NIAID · JOHNS HOPKINS UNIVERSITY · PI BROWN, TODD T, MARGOLICK, JOSEPH B. · 1993 to 2018
$61.5M
METHODOLOGICAL EXPERTISE IN INTREPRETING MACS DATAU01AI035043 · NIAID · JOHNS HOPKINS UNIVERSITY · PI JACOBSON, LISA P · 1993 to 2011
$26.9M
Center for the Analysis & Management of the Multicenter AIDS Cohort StudyUM1AI035043 · NIAID · JOHNS HOPKINS UNIVERSITY · PI D'SOUZA, GYPSYAMBER, JACOBSON, LISA P · 2012 to 2018
$20.7M
NCRR NIH HHS UL1 RR025005NIAID NIH HHS U01 AI035039NIAID NIH HHS U01 AI035040NIAID NIH HHS U01 AI035041NIAID NIH HHS U01 AI035042NIAID NIH HHS U01 AI035043NIAID NIH HHS UM1 AI035043
6 · The paper itself

Abstract

backgroundInfection with human immunodeficiency virus (HIV) influences the outcome and natural disease progression of hepatitis C virus (HCV) infection. While the majority of HCV mono-infected and HCV/HIV co-infected subjects develop chronic HCV infection, 20-46% of mono- and co-infected subjects spontaneously clear HCV infection. The mechanism underlying viral clearance is not clearly understood. Analysis of differential cellular gene expression (mRNA) between HIV-infected patients with persistent HCV infection or spontaneous clearance could provide a unique opportunity to decipher the mechanism of HCV clearance.

methodsPlasma RNA from HIV/HCV co-infected subjects who cleared HCV and those who remained chronically infected with HCV was sequenced using Ion Torrent technology. The sequencing results were analyzed to identify transcripts that are associated with HCV clearance by measuring differential gene expression in HIV/HCV co-infected subjects who cleared HCV and those who remained chronically infected with HCV.

resultsWe have identified plasma mRNA, the levels of which are significantly elevated (at least 5 fold, False Discovery Rate (FDR) <0.05) before HCV infection in subjects who cleared HCV compared to those who remained chronically infected. Upon further analysis of these differentially expressed genes, before and after HCV infection, we found that before HCV infection 12 genes were uniquely upregulated in the clearance group compared to the chronically infected group. Importantly, a number of these 12 genes and their upstream regulators (such as CCL3, IL17D, LBP, SOCS3, NFKBIL1, IRF) are associated with innate immune response functions.

conclusionsThese results suggest that subjects who spontaneously clear HCV may express these unique genes associated with innate immune functions.

Indexed as

CoinfectionFemaleGene Expression RegulationHepatitis CHepatitis C, ChronicHIV InfectionsHumansImmunity, InnateRNA, ViralViral LoadRNA, ViralChronic HCV infectionClearance of HCV infectionHIV/HCV coinfectionPlasma RNA sequencingSequence analysis

Identifiers

PMID27875997
PMCPMC5120459
OpenAlexW2553542352

What OpenQuestion holds

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LicenceCC BY
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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.