Evidence map›Paper›PMID 32431480›Full record

ArticleJournal of proteomics & bioinformatics2019

Quantitative Proteomics Using Formalin-fixed, Paraffin-embedded Biopsy Tissues in Inflammatory Disease.

Abhimanyu Amarnani, Joseph R Capri, Puneet Souda, David A Elashoff, Ivan A Lopez, Julian P Whitelegge, Ram R Singh

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

Article in Journal of proteomics & bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing papers in PubMed
0.9field-weighted citation impact, top 24% 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

7 citing papers in PubMed, 12 citations in OpenAlex.

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  6. Transcriptional and proteomic insights into the host response in fatal COVID-19 cases.Proceedings of the National Academy of Sciences of the United States of America · 2020
    Article
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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

7 authors at 1 institution in 1 country.

Abhimanyu AmarnaniDepartment of Head and Neck Surgery, UCLA, Los Angeles, CA 90095, USA.
Joseph R CapriThe Pasarow Mass Spectrometry Laboratory, Semel Institute for Neuroscience and Human Behavior, UCLA, Los Angeles, CA 90024, USA.
Puneet SoudaThe Pasarow Mass Spectrometry Laboratory, Semel Institute for Neuroscience and Human Behavior, UCLA, Los Angeles, CA 90024, USA.
David A ElashoffDepartment of Medicine/Statistics Core, UCLA, Los Angeles, CA 90095, USA.
Ivan A LopezDepartment of Head and Neck Surgery, UCLA, Los Angeles, CA 90095, USA.
Julian P WhiteleggeThe Pasarow Mass Spectrometry Laboratory, Semel Institute for Neuroscience and Human Behavior, UCLA, Los Angeles, CA 90024, USA.
Ram R SinghDepartment of Medicine/Rheumatology, UCLA, Los Angeles, CA 90095, USA.
University of California, Los Angeles · US

Funding

UCLA Clinical and Translational Science InstituteUL1TR000124 · NCATS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI DUBINETT, STEVEN M. · 2012 to 2015
$57.0M
UCLA Center for Biological RadioprotectorsU19AI067769 · NIAID · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI CHUTE, JOHN P, MCBRIDE, WILLIAM H. · 2005 to 2019
$44.6M
Transgenic & Knock-out MouseP30DK063491 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Andrea L Hevener · 2003 to 2026
$40.4M
Gender Bias in Lupus: Contribution of Sex ChromosomesR01AR056465 · NIAMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI SINGH, RAM RAJ · 2008 to 2012
$2.3M
Pathogenesis of Lupus DermatitisR01AI080778 · NIAID · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI SINGH, RAM RAJ · 2009 to 2013
$2.2M
Kidney Damage in Murine LupusR01AR050797 · NIAMS · UNIVERSITY OF CINCINNATI · PI SINGH, RAM RAJ · 2003 to 2006
$1.4M
NCATS NIH HHS UL1 TR000124NIAID NIH HHS R01 AI080778NIAID NIH HHS U19 AI067769NIAMS NIH HHS R01 AR050797NIAMS NIH HHS R01 AR056465NIDDK NIH HHS P30 DK063491
6 · The paper itself

Abstract

backgroundInvestigations in human disease pathogenesis have been hampered due to paucity of access to fresh-frozen tissues (FFT) for use in global, data-driven methodologies. As an alternative, formalin-fixed, paraffin-embedded (FFPE) tissues are readily available in pathology banks. However, the use of formalin for fixation can lead to the loss of proteins that appear during inflammation, thus introducing an inherent sample bias. To address this, we compared FF and FFPE tissue proteomics to determine whether FFPE-tissue can be used effectively in inflammatory diseases.

methodsAdjacent kidney slices from lupus nephritic mice were processed as FFPE or FFTs. Their tissue lysates were run together using proteomics workflow involving filter-aided sample preparation, in-solution dimethyl isotope labeling, StageTip fractionation, and nano-LC MS/MS through an Orbitrap XL MS.

resultsWe report a >97% concordance in protein identification between adjacent FFPE and FFTs in murine lupus nephritic kidneys. Specifically, proteins representing pathways, namely, 'systemic lupus erythematosus', 'interferon-α', 'TGF-β', and 'extracellular matrix', were reproducibly quantified between FFPE and FFTs. However, 12%-29% proteins were quantified differently in FFPE compared to FFTs, but the differences were consistent across experiments. In particular, certain proteins represented in pathways, including 'inflammatory response' and 'innate immune system' were quantified less in FFPE than in FFTs. In a pilot study of human FFPE tissues, we identified proteins relevant to pathogenesis in lupus nephritic kidney biopsies compared to control kidneys.

conclusionThis is the first report of lupus nephritis kidney proteomics using FFPE tissue. We concluded that archived FFPE tissues can be reliably used for proteomic analyses in inflammatory diseases, with a caveat that certain proteins related to immunity and inflammation may be quantified less in FFPE than in FFTs.

Indexed as

Formalin-fixed paraffin-embeddedFresh frozenInflammatory diseaseKidney biopsyLupus nephritisProteomics

Identifiers

PMID32431480
PMCPMC7236785
OpenAlexW2979238822

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.