Evidence map›Paper›PMID 40893776›Full record

ArticleBiochemistry and biophysics reports2025

Dual probe ligation in situ hybridization with rolling-circle amplification for high-plex spatial transcriptomics.

Sarah E Maguire, Joel Credle, Elizabeth M W Bertelson, Sunny Lee, Boyoung Cha, Dan Xie, Greg Kirk, Debjit Ray, Logan George, Aditya Suru and 5 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Biochemistry and biophysics reports, 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. 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

15 authors.

Sarah E MaguirePortal Bioscience, LLC, Baltimore, MD, 21205, USA.
Joel CredleInstitute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
Elizabeth M W BertelsonPortal Bioscience, LLC, Baltimore, MD, 21205, USA.
Sunny LeePortal Bioscience, LLC, Baltimore, MD, 21205, USA.
Boyoung ChaPortal Bioscience, LLC, Baltimore, MD, 21205, USA.
Dan XieApplied Materials Inc., 3050 Bowers Avenue, P.O. Box 58039, Santa Clara, CA, 95054, USA.
Greg KirkApplied Materials Inc., 3050 Bowers Avenue, P.O. Box 58039, Santa Clara, CA, 95054, USA.
Debjit RayApplied Materials Inc., 3050 Bowers Avenue, P.O. Box 58039, Santa Clara, CA, 95054, USA.
Logan GeorgeSidney Kimmel Comprehensive Cancer Center, Department of Oncology and the Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
Aditya SuruSidney Kimmel Comprehensive Cancer Center, Department of Oncology and the Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
Alexandre MaaloufSidney Kimmel Comprehensive Cancer Center, Department of Oncology and the Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
Chiseko IkenagaDepartment of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
Thomas LloydDepartment of Neurology, Baylor College of Medicine, Houston, TX, 77030, USA.
Nicolas J LlosaSidney Kimmel Comprehensive Cancer Center, Department of Oncology and the Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
H Benjamin LarmanInstitute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.

Funding

PROJECT 3: Applying Liquid Biopsy Technologies to Detect Clinical Response and Mechanisms of Resistance in the Treatment of LMSP50CA272170 · NCI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI JUDY E. GARBER · 2022 to 2026
$13.3M
NCI NIH HHS P50 CA272170
6 · The paper itself

Abstract

New biological insights are increasingly dependent upon a deeper understanding of tissue architectures. Critical to such studies are spatial transcriptomics technologies, especially those amenable to analysis of the most widely available human tissue type, formalin-fixed and paraffin-embedded (FFPE) clinical specimens. Here we build on our previous oligonucleotide probe ligation-based approach to accurately analyze FFPE mRNA, which suffers from variable levels of degradation. Ligation In Situ Hybridization followed by rolling circle amplification (LISH-Lock'n'Roll or LISH-LnR), provides a streamlined method to detect the spatial location of specific mRNA isoforms within FFPE tissue architectures. Iterative fluorescent probe hybridization and imaging enables highly multiplexed spatial transcriptomic studies, as demonstrated herein for fixed specimens from inclusion body myositis patients and pediatric rhabdomyosarcoma patients. We additionally demonstrate a system of molecular rheostats that can be used to fine tune the performance of the LISH-LnR assay. Combined with LISH-seq and LISH-QC, the LISH-LnR methodology provides a powerful toolkit for spatial transcriptomics.

Identifiers

PMID40893776
PMCPMC12391569

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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.