Evidence map›Paper›PMID 40549669›Full record

ArticleJournal of visualized experiments : JoVE2025

DNA-barcode-based Multiplex Immunofluorescence Imaging to Analyze FFPE Specimens from Genetically Reprogrammed Murine Melanoma.

Sachin S Surwase, Xin Ming M Zhou, Kathryn M Luly, Qingfeng Zhu, Niki Talebian, Robert A Anders, Jordan J Green, Stephany Y Tzeng, Joel C Sunshine

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PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of visualized experiments : JoVE, 2025. 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
–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

1 citing paper in PubMed.

  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

9 authors.

Sachin S Surwase *Department of Biomedical Engineering, Johns Hopkins University; Translational Tissue Engineering Center, Johns Hopkins University; Johns Hopkins Translational ImmunoEngineering Center, Johns Hopkins University.
Xin Ming M Zhou *Johns Hopkins Translational ImmunoEngineering Center, Johns Hopkins University; Department of Dermatology, Johns Hopkins University.
Kathryn M LulyDepartment of Biomedical Engineering, Johns Hopkins University; Translational Tissue Engineering Center, Johns Hopkins University; Johns Hopkins Translational ImmunoEngineering Center, Johns Hopkins University.
Qingfeng ZhuDepartment of Oncology, Johns Hopkins University; Department of Pathology, Johns Hopkins University; Convergence Institute, Sidney Kimmel Comprehensive Cancer Center Johns Hopkins University School of Medicine.
Niki TalebianDepartment of Pathology, Johns Hopkins University.
Robert A AndersDepartment of Oncology, Johns Hopkins University; Department of Pathology, Johns Hopkins University; Convergence Institute, Sidney Kimmel Comprehensive Cancer Center Johns Hopkins University School of Medicine; Bloomberg Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine.
Jordan J GreenDepartment of Biomedical Engineering, Johns Hopkins University; Translational Tissue Engineering Center, Johns Hopkins University; Johns Hopkins Translational ImmunoEngineering Center, Johns Hopkins University; Department of Oncology, Johns Hopkins University; Bloomberg Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine; Institute for Nanobiotechnology, Johns Hopkins University; Departments of Neurosurgery and Ophthalmology, Johns Hopkins University School of Medicine; Departments of Materials Science & Engineering and Chemical & Biomolecular Engineering, Johns Hopkins University.
Stephany Y TzengDepartment of Biomedical Engineering, Johns Hopkins University; Translational Tissue Engineering Center, Johns Hopkins University; Johns Hopkins Translational ImmunoEngineering Center, Johns Hopkins University.
Joel C SunshineDepartment of Biomedical Engineering, Johns Hopkins University; Johns Hopkins Translational ImmunoEngineering Center, Johns Hopkins University; Department of Dermatology, Johns Hopkins University; Department of Oncology, Johns Hopkins University; Department of Pathology, Johns Hopkins University; Bloomberg Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine; joelsunshine@jhmi.edu.

Funding

Translational Research Central ServicesP30CA006973 · NCI · JOHNS HOPKINS UNIVERSITY · PI ALAN KEITH MEEKER · 1985 to 2026
$208.6M
TR&D Project 3P41EB028239 · NIBIB · JOHNS HOPKINS UNIVERSITY · PI Jordan Green, JONATHAN P SCHNECK · 2019 to 2026
$11.5M
A PLATFORM TECHNOLOGY TO GENETICALLY REPROGRAM CANCER CELLS FOR ENHANCED IMMUNOTHERAPYR37CA246699 · NCI · JOHNS HOPKINS UNIVERSITY · PI TZENG, STEPHANY YI · 2020 to 2025
$2.6M
Gene Delivery Nanoparticles to Treat GlioblastomaR01CA228133 · NCI · JOHNS HOPKINS UNIVERSITY · PI GREEN, JORDAN · 2019 to 2023
$1.9M
NCI NIH HHS P30 CA006973NCI NIH HHS R01 CA228133NCI NIH HHS R37 CA246699NIBIB NIH HHS P41 EB028239
6 · The paper itself

Abstract

Presented here is an emerging DNA-barcode-based multiplex imaging technique based on Co-Detection-by-indEXing that analyzes the spatial proteomics of tissue microenvironments. Successful imaging requires a repertoire of well-designed and properly validated antibody panels, but very few currently exist for formalin-fixed paraffin-embedded (FFPE) samples. FFPE offers several advantages over fresh-frozen specimens, such as widespread availability, ease of handling and storage, and the ability to make tissue microarrays (TMAs). Here, we present a protocol to develop an antibody panel for visualizing and analyzing FFPE tissues from a murine melanoma model treated with nanoparticles, which deliver plasmid DNA encoding immunologic signals for tumor microenvironment reprogramming. We also describe an image analysis pipeline using open-source computational tools for annotating tissues, segmenting cells, processing proteomics data, phenotyping cell populations, and quantifying spatial metrics. The protocol offers applications for designing antibody panels in murine FFPE and generating novel insights into the spatial proteomics of complex tissue microenvironments.

Indexed as

DNAFluorescent Antibody TechniqueMelanomaMelanoma, ExperimentalAnimalsFormaldehydeMiceParaffin EmbeddingTissue FixationTumor MicroenvironmentDNAFormaldehyde

Identifiers

PMID40549669
PMCPMC13198906

What Socratic holds

Textmetadata
LicenceTDM
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 Socratic graph.