Evidence map›Paper›PMID 29378643›Full record

ArticleGenome biology2018

A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers.

Enrique Martin-Gayo, Michael B Cole, Kellie E Kolb, Zhengyu Ouyang, Jacqueline Cronin, Samuel W Kazer, Jose Ordovas-Montanes, Mathias Lichterfeld, Bruce D Walker, Nir Yosef and 2 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.

0numbers the graph read from it
0cells of the map it votes in
34citing papers in PubMed
–field-weighted citation impact
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

34 citing papers in PubMed.

  1. Article
  2. Observational
  3. Review
  4. Advances in Single-Cell Sequencing for Infectious Diseases: Progress and Perspectives.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025
    Review
  5. Observational
  6. HIV controllers: hope for a functional cure.Frontiers in immunology · 2025
    Review
  7. Article
  8. Article
  9. Review
  10. Article
  11. Review
  12. Article
  13. Article
  14. Article
  15. Article
  16. Article
  17. Article
  18. Review
  19. Review
  20. Review
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.

Enrique Martin-GayoRagon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
Michael B ColeDepartment of Physics, University of California, Berkeley, CA, USA.
Kellie E KolbRagon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
Zhengyu OuyangRagon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
Jacqueline CroninRagon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
Samuel W KazerRagon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
Jose Ordovas-MontanesRagon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
Mathias LichterfeldRagon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
Bruce D WalkerRagon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
Nir YosefRagon Institute of MGH, MIT and Harvard, Cambridge, MA, USA. niryosef@berkeley.edu.
Alex K ShalekRagon Institute of MGH, MIT and Harvard, Cambridge, MA, USA. shalek@mit.edu.
Xu G YuRagon Institute of MGH, MIT and Harvard, Cambridge, MA, USA. xyu@mgh.harvard.edu.

Funding

The impact of HIV viral diversity and cellular immunity on HIV pathogenesisP30AI060354 · NIAID · HARVARD UNIVERSITY (MEDICAL SCHOOL) · PI ROBERT A. PARKER · 2004 to 2026
$94.4M
Systems investigation of vaccine responses in B cell depleted autoimmune patientsU19AI089992 · NIAID · YALE UNIVERSITY · PI David A. Hafler, RUTH R MONTGOMERY · 2010 to 2026
$50.4M
Center for Cell CircuitsRM1HG006193 · NHGRI · BROAD INSTITUTE, INC. · PI BLAINEY, PAUL CLARK, HACOHEN, NIR · 2016 to 2020
$14.9M
Novel Biologic Therapies for GVHDR01HL095791 · NHLBI · SEATTLE CHILDREN'S HOSPITAL · PI KEAN, LESLIE S · 2010 to 2025
$13.3M
Rules of gene expression modeled on human dendritic cell response to pathogensU01HG007910 · NHGRI · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI GARBER, MANUEL, LUBAN, JEREMY · 2015 to 2017
$6.1M
Classification of Cortical Neurons by Single Cell TranscriptomicsU01MH105979 · NIMH · UNIVERSITY OF CALIFORNIA BERKELEY · PI NGAI, JOHN J. · 2014 to 2016
$4.5M
Immunoregulatory Function of Myelomonocytic Receptors in HIV-1 InfectionR01AI078799 · NIAID · MASSACHUSETTS GENERAL HOSPITAL · PI YU, XU · 2008 to 2017
$4.1M
"Bottom - Up" Profiling of Interacting Cellular SystemsDP2GM119419 · NIGMS · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI SHALEK, ALEX K · 2015 to 2015
$2.3M
Molecular basis of myelomonocytic receptor function in HIV-1 infectionR01AI087452 · NIAID · UNIVERSITY OF MARYLAND BALTIMORE · PI SUNDBERG, ERIC JOHN · 2010 to 2014
$2.1M
An integrated multiplexed genomic assay for low input clinical samples1U24AI118672 · NIAID · BROAD INSTITUTE, INC. · PI SHALEK, ALEX K · 2015 to 2019
$2.0M
Inhibitors of host kinases as molecular targets for immune defense against HIV-1R01AI098487 · NIAID · MASSACHUSETTS GENERAL HOSPITAL · PI LICHTERFELD, MATHIAS · 2012 to 2015
$1.7M
A Microengraving Technology for the Study of Latently HIV-infected Primary CellsR01AI089339 · NIAID · MASSACHUSETTS GENERAL HOSPITAL · PI YU, XU · 2010 to 2013
$1.6M
Arnold and Mabel Beckman Foundation Beckman Young Investigator ProgramBill and Melinda Gates Foundation OPP 1066973Division of Intramural Research, National Institute of Allergy and Infectious Diseases AI116228Kinship Foundation Searle Scholars ProgramNational Institute of Allergy and Infectious Diseases 2U19AI089992National Institute of Allergy and Infectious Diseases 5U24AI118672National Science Foundation GRFPNHGRI NIH HHS 2RM1HG006193NHGRI NIH HHS RM1 HG006193NHGRI NIH HHS U01 HG007910NHGRI NIH HHS U01HG007910NHLBI NIH HHS 2R01HL095791NHLBI NIH HHS HL121890NHLBI NIH HHS R01 HL095791NHLBI NIH HHS R21 HL121890NHLBI NIH HHS R56 HL126554NIAID NIH HHS P30 AI060354NIAID NIH HHS R01 AI078799NIAID NIH HHS R01 AI087452NIAID NIH HHS R01 AI089339NIAID NIH HHS R01 AI098487NIAID NIH HHS R21 AI106468NIAID NIH HHS R21 AI116228NIAID NIH HHS R33 AI116228NIAID NIH HHS R56 AI098484NIAID NIH HHS U19 AI089992NIAID NIH HHS U24 AI118672NIDCR NIH HHS F31 DE025176NIGMS NIH HHS DP2 GM119419NIGMS NIH HHS DP2OD020839NIH HHS F31DE025176-01NIMH NIH HHS U01 MH105979NIMH NIH HHS U01MH105979
6 · The paper itself

Abstract

backgroundHuman immunity relies on the coordinated responses of many cellular subsets and functional states. Inter-individual variations in cellular composition and communication could thus potentially alter host protection. Here, we explore this hypothesis by applying single-cell RNA-sequencing to examine viral responses among the dendritic cells (DCs) of three elite controllers (ECs) of HIV-1 infection.

resultsTo overcome the potentially confounding effects of donor-to-donor variability, we present a generally applicable computational framework for identifying reproducible patterns in gene expression across donors who share a unifying classification. Applying it, we discover a highly functional antiviral DC state in ECs whose fractional abundance after in vitro exposure to HIV-1 correlates with higher CD4

conclusionsOverall, our results demonstrate how single-cell approaches can reveal previously unappreciated, yet important, immune behaviors and empower rational frameworks for modulating systems-level immune responses that may prove therapeutically and prophylactically useful.

Indexed as

HIV-1Sequence Analysis, RNABiomarkersDendritic CellsGene Expression ProfilingGenomicsHIV InfectionsHumansReproducibility of ResultsSingle-Cell AnalysisBiomarkersAdjuvantDendritic cellDifferential expressionElite controllerHIV-1ReproducibilitySingle-cell genomicsSingle-cell RNA-seq

Identifiers

PMID29378643
PMCPMC5789701

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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.