Evidence map›Paper›PMID 40233746›Full record

ArticleCell genomics2025

Enhanced interpretation of immune cell phenotype and function through a rhesus macaque single-cell atlas.

Eisa Mahyari, Gregory J Boggy, G W McElfresh, Maanasa Kaza, Sebastian Benjamin, Benjamin Varco-Merth, Sohita Ojha, Shana Feltham, William Goodwin, Candice Nkoy and 12 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell genomics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing 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

6 citing papers in PubMed.

  1. Article
  2. Article
  3. Review
  4. Article
  5. Article
  6. 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

22 authors.

Eisa MahyariOregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA.
Gregory J BoggyOregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA.
G W McElfreshOregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA.
Maanasa KazaOregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA.
Sebastian BenjaminOregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA.
Benjamin Varco-MerthOregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA; Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA.
Sohita OjhaVaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA.
Shana FelthamVaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA.
William GoodwinOregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA; Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA.
Candice NkoyOregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA; Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA.
Derick DuellOregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA; Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA.
Andrea SelsethVaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA.
Tyler BennettVaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA.
Aaron Barber-AxthelmVaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA.
Jeremy V SmedleyOregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA; Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA.
Caralyn S LabriolaOregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA; Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA.
Michael K AxthelmOregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA; Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA.
R Keith ReevesDivision of Innate and Comparative Immunology, Center for Human Systems Immunology, Duke University School of Medicine, Durham, NC, USA; Department of Surgery, Duke University School of Medicine, Durham, NC, USA.
Afam A OkoyeOregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA; Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA.
Scott G HansenOregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA; Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA.
Louis J PickerOregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA; Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA.
Benjamin N BimberOregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA; Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA. Electronic address: bimber@ohsu.edu.

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
Project 3: Determination of the minimal MHC-E-restricted SIV epitope targeting required for RhCMV/SIV vaccine-mediated SIV replication arrest efficacyP01AI174856 · NIAID · OREGON HEALTH & SCIENCE UNIVERSITY · PI Louis J. Picker · 2022 to 2026
$29.9M
Fine Mechanisms of Adaptive NK Cell Formation Against HIV and SIVR01AI161010 · NIAID · DUKE UNIVERSITY · PI JOST, STEPHANIE, REEVES, ROGER KEITH · 2021 to 2025
$4.9M
NIAID NIH HHS P01 AI174856NIAID NIH HHS R01 AI161010NIH HHS P51 OD011092
6 · The paper itself

Abstract

Single-cell RNA sequencing (scRNA-seq) allows cell classification using genome-wide transcriptional state; however, high-dimensional transcriptomic profiles, and the unsupervised analyses employed to interpret them, provide a systematically different view of biology than well-established functional/lineage definitions of immunocytes. Understanding these differences and limits is essential for accurate interpretation of these rich data. We present the Rhesus Immune Reference Atlas (RIRA), the first immune-focused macaque single-cell multi-tissue atlas. We contrasted transcriptional profiles against immune lineages, using surface protein and marker genes as ground truth. While the pattern of clustering can align with cell type, this is not always true. Especially within T and natural killer (NK) cells, many functionally distinct subsets lack defining markers, and strong shared expression programs, such as cytotoxicity, result in systematic intermingling by unsupervised clustering. We identified gene programs with high discriminatory/diagnostic value, including multi-gene signatures that model T/NK cell maturation. Directly measuring these diagnostic programs complements unsupervised analyses.

Indexed as

Macaca mulattaSingle-Cell AnalysisAnimalsCluster AnalysisGene Expression ProfilingKiller Cells, NaturalPhenotypeSequence Analysis, RNAT-LymphocytesTranscriptomeimmunologyrhesus macaquesingle-cell RNA-seqT cells

Identifiers

PMID40233746
PMCPMC12143338

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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.