Evidence map›Paper›PMID 31481502›Full record

ArticleCancer research2019

Quantification and Localization of Protein-RNA Interactions in Patient-Derived Archival Tumor Tissue.

Emmeline L Blanchard, Danae Argyropoulou, Chiara Zurla, Sushma M Bhosle, Daryll Vanover, Philip J Santangelo

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

Article in Cancer research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
0.2field-weighted citation impact, top 47% 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

5 citing papers in PubMed, 7 citations in OpenAlex.

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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

6 authors at 1 institution in 1 country.

Emmeline L BlanchardWallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia.
Danae ArgyropoulouWallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia.
Chiara ZurlaWallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia.
Sushma M BhosleWallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia.
Daryll VanoverWallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia.
Philip J SantangeloWallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia.ORCID 0000-0001-7352-0339
Georgia Institute of Technology · US

Funding

Graduate Training for Rationally Designed, Integrative Biomaterials - GT BioMATT32EB006343 · NIBIB · GEORGIA INSTITUTE OF TECHNOLOGY · PI TEMENOFF, JOHNNA S · 2008 to 2018
$2.2M
Single RNA sensitive probes for studying viral replication and buddingR01GM094198 · NIGMS · GEORGIA INSTITUTE OF TECHNOLOGY · PI SANTANGELO, PHILIP J · 2010 to 2014
$2.0M
Characterizing gene regulation with single molecule sensitive probesR21CA147922 · NCI · GEORGIA INSTITUTE OF TECHNOLOGY · PI SANTANGELO, PHILIP J · 2011 to 2013
$467k
NCI NIH HHS R21 CA147922NIBIB NIH HHS T32 EB006343NIGMS NIH HHS R01 GM094198
6 · The paper itself

Abstract

Abnormal post-transcriptional regulation induced by alterations of mRNA-protein interactions is critical during tumorigenesis and cancer progression and is a hallmark of cancer cells. A more thorough understanding is needed to develop treatments and foresee outcomes. Cellular and mouse tumor models are insufficient for vigorous investigation as they lack consistency and translatability to humans. Moreover, to date, studies in human tumor tissue are predominately limited to expression analysis of proteins and mRNA, which do not necessarily provide information about the frequency of mRNA-protein interactions. Here, we demonstrate novel optimization of a method that is based on FISH and proximity ligation techniques to quantify mRNA interactions with RNA-binding proteins relevant for tumorigenesis and cancer progression in archival patient-derived tumor tissue. This method was validated for multiple mRNA-protein pairs in several cellular models and in multiple types of archival human tumor samples. Furthermore, this approach allowed high-throughput analysis of mRNA-protein interactions across a wide range of tumor types and stages through tumor microarrays. This method is quantitative, specific, and sensitive for detecting interactions and their localization at both the individual cell and whole-tissue scales with single interaction sensitivity. This work presents an important tool in investigating post-transcriptional regulation in cancer on a high-throughput scale, with great potential for translatability into any applications where mRNA-protein interactions are of interest. SIGNIFICANCE: This work presents an approach to sensitively, specifically, and quantitatively detect and localize native mRNA and protein interactions for analysis of abnormal post-transcriptional regulation in patient-derived archival tumor samples.

Indexed as

RNA Processing, Post-TranscriptionalAnimalsBiological Specimen BanksCell Line, TumorChlorocebus aethiopsColonic NeoplasmsFluorescent DyesHigh-Throughput Screening AssaysHumansIn Situ Hybridization, FluorescenceLung NeoplasmsMiceMicroscopy, FluorescenceNeoplasm ProteinsRNA-Binding ProteinsRNA, MessengerFluorescent DyesNeoplasm ProteinsRNA-Binding ProteinsRNA, MessengerRNA, Neoplasm

Identifiers

PMID31481502
PMCPMC6801105
OpenAlexW2971407811

What OpenQuestion 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 OpenQuestion graph.