Evidence map›Paper›PMID 38545822›Full record

ArticleJournal of extracellular vesicles2024

Identification and validation of extracellular vesicle reference genes for the normalization of RT-qPCR data.

Cláudio Pinheiro, Niké Guilbert, Lien Lippens, Quentin Roux, Robin Boiy, Suzanne Fischer, Sofie Van Dorpe, Bram De Craene, Geert Berx, Tom Boterberg and 7 more

Open access · goldAbstract read
In one paragraph

Article in Journal of extracellular vesicles, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
25citing papers in PubMed, 1 pooled it
7.0field-weighted citation impact, top 2% 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

25 citing papers in PubMed, 1 synthesis or guideline pooled it, 30 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

17 authors at 4 institutions in 2 countries.

Cláudio PinheiroLaboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium.ORCID https://orcid.org/0000-0003-1834-199X
Niké GuilbertLaboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium.
Lien LippensLaboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium.
Quentin RouxLaboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium.ORCID https://orcid.org/0000-0001-8720-1427
Robin BoiyLaboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium.
Suzanne FischerLaboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium.ORCID https://orcid.org/0000-0002-1714-556X
Sofie Van DorpeLaboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium.ORCID https://orcid.org/0000-0003-0533-7561
Bram De CraeneCancer Research Institute Ghent (CRIG), Ghent, Belgium.
Geert BerxCancer Research Institute Ghent (CRIG), Ghent, Belgium.
Tom BoterbergDepartment of Radiation Oncology, Ghent University Hospital, Ghent, Belgium.
Gwen SysDepartment of Orthopedics and Traumatology, Ghent University Hospital, Ghent, Belgium.
Hannelore DenysCancer Research Institute Ghent (CRIG), Ghent, Belgium.
Ilkka MiinalainenBiocenter Oulu, University of Oulu, Oulu, Finland.
Pieter MestdaghCancer Research Institute Ghent (CRIG), Ghent, Belgium.
Jo VandesompeleCancer Research Institute Ghent (CRIG), Ghent, Belgium.
Olivier De WeverLaboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium.
An HendrixLaboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium.
Ghent University · BEGhent University Hospital · BEiMinds · BEUniversity of Oulu · FI

Funding

Fonds Wetenschappelijk OnderzoekH2020 Marie Skłodowska-Curie Actions 722148Kom op tegen KankerUniversiteit Gent
6 · The paper itself

Abstract

Extracellular vesicles (EVs) contain a plethora of biomolecules, including nucleic acids, with diverse diagnostic and therapeutic application potential. Although reverse transcription-quantitative PCR (RT-qPCR) is the most widely applied laboratory technique to evaluate gene expression, its applicability in EV research is challenged by the lack of universal and stably present reference genes (RGs). In this study, we identify, validate and establish SNRPG, OST4, TOMM7 and NOP10 as RGs for the normalization of EV-associated genes by RT-qPCR. We show the stable presence of SNRPG, OST4, TOMM7 and NOP10 in multiple cell lines and their secreted EVs (n = 12) under different (patho)physiological conditions as well as in human-derived biofluids (n = 3). Enzymatic treatments confirm the presence of SNRPG, OST4, TOMM7 and NOP10 inside EVs. In addition, the four EV-associated RGs are stably detected in a size-range of EV subpopulations. RefFinder analysis reveals that SNRPG, OST4, TOMM7 and NOP10 are more stable compared to RGs established specifically for cultured cells or tissues such as HMBS, YWHAZ, SDHA and GAPDH. In summary, we present four universal and stably present EV-associated RGs to enable normalization and thus steer the implementation of RT-qPCR for the analysis of EV-associated RNA cargo for research or clinical applications.

Indexed as

Extracellular VesiclesReverse TranscriptionCell LineCells, CulturedHumansRNAsnRNP Core ProteinsRNAsnRNP Core ProteinsSNRPG protein, humanbloodconditioned mediumexosomesextracellular vesiclesmicrovesiclesmRNAproteasereference genesRNasetissueurine

Identifiers

PMID38545822
PMCPMC10974686
OpenAlexW4393264774

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.