Evidence map›Paper›PMID 35447093›Full record

ArticleImmunity2022

Combined protein and nucleic acid imaging reveals virus-dependent B cell and macrophage immunosuppression of tissue microenvironments.

Sizun Jiang, Chi Ngai Chan, Xavier Rovira-Clavé, Han Chen, Yunhao Bai, Bokai Zhu, Erin McCaffrey, Noah F Greenwald, Candace Liu, Graham L Barlow and 22 more

Open access · hybridAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Immunity, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.

0numbers the graph read from it
0cells of the map it votes in
66citing papers in PubMed
13.6field-weighted citation impact, top 1% 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

66 citing papers in PubMed, 89 citations in OpenAlex.

  1. Article
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  13. Roadmap for spatial transcriptomics of HIV in tissues.Current opinion in HIV and AIDS · 2025
    Review
  14. Review
  15. Analysis of Hyperexpanded T Cell Clones in SARS-CoV-2 Vaccine-Associated Liver Injury by Spatial Proteomics and Transcriptomics.Liver international : official journal of the International Association for the Study of the Liver · 2025
    Article
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6 more citing papers are in PubMed but not listed here.

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

32 authors at 7 institutions in 4 countries.

Sizun JiangDepartment of Pathology, Stanford University, Stanford, CA, USA; Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA. Electronic address: sjiang3@bidmc.harvard.edu.
Chi Ngai ChanVaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA.
Xavier Rovira-ClavéDepartment of Pathology, Stanford University, Stanford, CA, USA.
Han ChenDepartment of Pathology, Stanford University, Stanford, CA, USA.
Yunhao BaiDepartment of Pathology, Stanford University, Stanford, CA, USA.
Bokai ZhuDepartment of Pathology, Stanford University, Stanford, CA, USA.
Erin McCaffreyDepartment of Pathology, Stanford University, Stanford, CA, USA.
Noah F GreenwaldDepartment of Pathology, Stanford University, Stanford, CA, USA.
Candace LiuDepartment of Pathology, Stanford University, Stanford, CA, USA.
Graham L BarlowDepartment of Pathology, Stanford University, Stanford, CA, USA.
Jason L WeiratherCenter of Immuno-Oncology, Dana-Faber Cancer Institute, Boston, MA, USA.
John Paul OliveriaDepartment of Pathology, Stanford University, Stanford, CA, USA; Department of Medicine, McMaster University, Hamilton, ON, Canada.
Tsuguhisa NakayamaDepartment of Pathology, Stanford University, Stanford, CA, USA; Department of Otorhinolaryngology, Jikei University School of Medicine, Tokyo, Japan.
Ivan T LeeDepartment of Pathology, Stanford University, Stanford, CA, USA; Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
Matthias S MatterPathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland.
Anne E CarlisleCenter of Immuno-Oncology, Dana-Faber Cancer Institute, Boston, MA, USA.
Darci PhilipsDepartment of Pathology, Stanford University, Stanford, CA, USA.
Gustavo VazquezDepartment of Pathology, Stanford University, Stanford, CA, USA.
Nilanjan MukherjeeDepartment of Pathology, Stanford University, Stanford, CA, USA.
Kathleen Busman-SahayVaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA.
Michael NekorchukVaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA.
Margaret TerryVaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA.
Skyler YoungerVaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA.
Marc BosseDepartment of Pathology, Stanford University, Stanford, CA, USA.
Janos DemeterDepartment of Pathology, Stanford University, Stanford, CA, USA.
Scott J RodigDepartment of Pathology, Brigham & Women's Hospital, Boston, MA, USA.
Alexandar TzankovPathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland.
Yury GoltsevDepartment of Pathology, Stanford University, Stanford, CA, USA.
David Robert McIlwainDepartment of Pathology, Stanford University, Stanford, CA, USA.
Michael AngeloDepartment of Pathology, Stanford University, Stanford, CA, USA.
Jacob D EstesVaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA; Division of Pathobiology & Immunology, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA. Electronic address: estesja@ohsu.edu.
Garry P NolanDepartment of Pathology, Stanford University, Stanford, CA, USA. Electronic address: gnolan@stanford.edu.
Stanford University · USChildren's Cancer Therapy Development Institute · USDana-Farber Cancer Institute · USOregon Health & Science University · USUniversity of Basel · CHBrigham and Women's Hospital · USOregon National Primate Research Center · US

Funding

Upgrade of confocal microscopy at the Oregon National Primate Research CenterP51OD011092 · OD · OREGON HEALTH & SCIENCE UNIVERSITY · PI Bonnie J. Nagel · 2012 to 2026
$203.9M
Collaboratory of AIDS Researchers for Eradication (CARE)UM1AI164567 · NIAID · UNIV OF NORTH CAROLINA CHAPEL HILL · PI DAVID M. MARGOLIS · 2021 to 2026
$31.6M
MOLECULAR &CELLULAR IMMUNOBIOLOGYT32AI007290 · NIAID · STANFORD UNIVERSITY · PI Sean Curtis Bendall, Olivia M Martinez · 1985 to 2026
$27.0M
Defining Mechanisms of Viral Persistence in Situ at the Single-Cell LevelR01AI149672 · NIAID · OREGON HEALTH & SCIENCE UNIVERSITY · PI ESTES, JACOB D · 2020 to 2024
$4.0M
Predicting response to anti-PD-1 therapy in triple negative breast cancer by comprehensive profiling of the tumor microenvironmentF31CA246880 · NCI · STANFORD UNIVERSITY · PI GREENWALD, NOAH · 2020 to 2021
$53k
NCI NIH HHS F31 CA246880NIAID NIH HHS R01 AI149672NIAID NIH HHS T32 AI007290NIAID NIH HHS UM1 AI164567NIH HHS P51 OD011092
6 · The paper itself

Abstract

Understanding the mechanisms of HIV tissue persistence necessitates the ability to visualize tissue microenvironments where infected cells reside; however, technological barriers limit our ability to dissect the cellular components of these HIV reservoirs. Here, we developed protein and nucleic acid in situ imaging (PANINI) to simultaneously quantify DNA, RNA, and protein levels within these tissue compartments. By coupling PANINI with multiplexed ion beam imaging (MIBI), we measured over 30 parameters simultaneously across archival lymphoid tissues from healthy or simian immunodeficiency virus (SIV)-infected nonhuman primates. PANINI enabled the spatial dissection of cellular phenotypes, functional markers, and viral events resulting from infection. SIV infection induced IL-10 expression in lymphoid B cells, which correlated with local macrophage M2 polarization. This highlights a potential viral mechanism for conditioning an immunosuppressive tissue environment for virion production. The spatial multimodal framework here can be extended to decipher tissue responses in other infectious diseases and tumor biology.

Indexed as

HIV InfectionsNucleic AcidsSimian Acquired Immunodeficiency SyndromeSimian Immunodeficiency VirusAnimalsCD4-Positive T-LymphocytesDNA VirusesImmunosuppression TherapyMacaca mulattaMacrophagesViral LoadNucleic AcidsHIVimmunosuppressionmultiplexed imagingsingle-cell biologySIVspatial multiomicsviral pathogenesisviral reservoirvirus-host interactions

Identifiers

PMID35447093
PMCPMC9220319
OpenAlexW4224249440

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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.