Evidence map›Paper›PMID 40728999›Full record

ArticleCurrent issues in molecular biology2025

A New Tool to Decrease Interobserver Variability in Biomarker Annotation in Solid Tumor Tissue for Spatial Transcriptomic Analysis.

Sravya Palavalasa, Emily Baker, Jack Freeman, Aditri Gokul, Weihua Zhou, Dafydd Thomas, Wajd N Al-Holou, Meredith A Morgan, Theodore S Lawrence, Daniel R Wahl

Abstract read
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In one paragraph

Article in Current issues in molecular biology, 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

10 authors.

Sravya PalavalasaDepartment of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA.ORCID 0000-0001-5276-3972
Emily BakerDepartment of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA.
Jack FreemanDepartment of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA.
Aditri GokulDepartment of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA.
Weihua ZhouDepartment of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA.
Dafydd ThomasRogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA.
Wajd N Al-HolouDepartment of Neurosurgery, University of Michigan, Ann Arbor, MI 48109, USA.
Meredith A MorganDepartment of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA.
Theodore S LawrenceDepartment of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA.
Daniel R WahlDepartment of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA.

Funding

Targeting Nucleotide Metabolism to Overcome Therapy Resistance in GlioblastomaR37CA258346 · NCI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Daniel R Wahl · 2021 to 2026
$3.3M
De Novo Nucleotide Synthesis as a Mediator of Radiation Resistance and a Therapeutic Target in GlioblastomaK08CA234416 · NCI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI WAHL, DANIEL R · 2019 to 2023
$1.1M
Defining Tumor Microenvironmental Interactions that drive THY1-Mediated Treatment Resistance in GlioblastomaK08NS128271 · NINDS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Wajd Al-Holou · 2024 to 2026
$700k
American Cancer Society PF-23-1077428-01-MMCancer Center Support grant P30CA46592Damon Runyon Cancer Research Foundation Clinical Investigator awardIvy Foundation Ben and Catherine Ivy foundation emerging leader grant awardNCI NIH HHS K08CA234416NCI NIH HHS R37CA258346NIH HHS 1R01CA240515-20NINDS NIH HHS K08 NS128271Sontag Foundation Distinguished Science AwardSPORE grant P50CA269022U-M Rogel Cancer Center Munn Team Science Catalyst Award
6 · The paper itself

Abstract

Integrating spatial transcriptomic data with immunofluorescence image data is challenging using existing tools due to their differences in spatial resolution. Immunofluorescence provides information about protein expression at the cellular or subcellular level, whereas spatial transcriptomic platforms typically rely on multicellular "spots" for RNA profiling. Our study coupled spatial transcriptomics of irradiated glioblastoma tissues with immunofluorescence for γH2AX, a marker of DNA damage within the nuclei of cells. We then compared gene expression in γH2AX-positive and negative regions within the tissue. There was significant interobserver variability in manual annotation of γH2AX positivity in multicellular spots by three different researchers (Kappa statistic = 0.345), despite all of them being familiar with γH2AX immunofluorescence and having predefined imaging parameters for annotation. This variability led to different researchers nominating different genes as being associated with DNA repair. To overcome this problem, we have developed a new tool using MATLAB. This tool performs "spot"-wise image analysis and uses researcher-defined parameters such as immunofluorescent marker intensity threshold and number of positive cells to annotate the "spots" as γH2AX positive or negative. The tissue with the most variability in manual annotation was annotated reproducibly by our MATLAB tool, leading to reproducible downstream analysis.

Indexed as

immunofluorescent image analysisinterobserver variabilityspatial transcriptomics

Identifiers

PMID40728999
PMCPMC12293790

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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.