Evidence map›Paper›PMID 24687888›Full record

ArticleMolecular & cellular proteomics : MCP2014

Discovery of colorectal cancer biomarker candidates by membrane proteomic analysis and subsequent verification using selected reaction monitoring (SRM) and tissue microarray (TMA) analysis.

Hideaki Kume, Satoshi Muraoka, Takahisa Kuga, Jun Adachi, Ryohei Narumi, Shio Watanabe, Masayoshi Kuwano, Yoshio Kodera, Kazuyuki Matsushita, Junya Fukuoka and 5 more

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

Article in Molecular & cellular proteomics : MCP, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.

0numbers the graph read from it
0cells of the map it votes in
35citing papers in PubMed
4.2field-weighted citation impact, top 5% 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

35 citing papers in PubMed, 129 citations in OpenAlex.

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  15. Disease markers · 2022
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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

15 authors at 6 institutions in 1 country.

Hideaki KumeFrom the ‡Laboratory of Proteome Research, National Institute of Biomedical Innovation, Osaka, Japan;
Satoshi MuraokaFrom the ‡Laboratory of Proteome Research, National Institute of Biomedical Innovation, Osaka, Japan;
Takahisa KugaFrom the ‡Laboratory of Proteome Research, National Institute of Biomedical Innovation, Osaka, Japan;
Jun AdachiFrom the ‡Laboratory of Proteome Research, National Institute of Biomedical Innovation, Osaka, Japan;
Ryohei NarumiFrom the ‡Laboratory of Proteome Research, National Institute of Biomedical Innovation, Osaka, Japan;
Shio WatanabeFrom the ‡Laboratory of Proteome Research, National Institute of Biomedical Innovation, Osaka, Japan;
Masayoshi KuwanoFrom the ‡Laboratory of Proteome Research, National Institute of Biomedical Innovation, Osaka, Japan;
Yoshio Kodera§Laboratory of Biomolecular Dynamics, Department of Physics, Kitasato University School of Science, Kanagawa, Japan;
Kazuyuki Matsushita¶Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan; ‖Clinical Proteomics Research Center, Chiba University Hospital, Chiba, Japan;
Junya Fukuoka**Department of Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan;
Takeshi Masuda‡‡Institute for Advanced Biosciences, Keio University, Yamagata, Japan;
Yasushi Ishihama§§Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan;
Hisahiro Matsubara¶¶Department of Frontier Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan.
Fumio Nomura¶Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan; ‖Clinical Proteomics Research Center, Chiba University Hospital, Chiba, Japan;
Takeshi TomonagaFrom the ‡Laboratory of Proteome Research, National Institute of Biomedical Innovation, Osaka, Japan; tomonaga@nibio.go.jp.
National Institute of Biomedical Innovation, Health and Nutrition · JPChiba University · JPKitasato University · JPKyoto University · JPNagasaki University · JPYamagata University · JP

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Recent advances in quantitative proteomic technology have enabled the large-scale validation of biomarkers. We here performed a quantitative proteomic analysis of membrane fractions from colorectal cancer tissue to discover biomarker candidates, and then extensively validated the candidate proteins identified. A total of 5566 proteins were identified in six tissue samples, each of which was obtained from polyps and cancer with and without metastasis. GO cellular component analysis predicted that 3087 of these proteins were membrane proteins, whereas TMHMM algorithm predicted that 1567 proteins had a transmembrane domain. Differences were observed in the expression of 159 membrane proteins and 55 extracellular proteins between polyps and cancer without metastasis, while the expression of 32 membrane proteins and 17 extracellular proteins differed between cancer with and without metastasis. A total of 105 of these biomarker candidates were quantitated using selected (or multiple) reaction monitoring (SRM/MRM) with stable synthetic isotope-labeled peptides as an internal control. The results obtained revealed differences in the expression of 69 of these proteins, and this was subsequently verified in an independent set of patient samples (polyps (n = 10), cancer without metastasis (n = 10), cancer with metastasis (n = 10)). Significant differences were observed in the expression of 44 of these proteins, including ITGA5, GPRC5A, PDGFRB, and TFRC, which have already been shown to be overexpressed in colorectal cancer, as well as proteins with unknown function, such as C8orf55. The expression of C8orf55 was also shown to be high not only in colorectal cancer, but also in several cancer tissues using a multicancer tissue microarray, which included 1150 cores from 14 cancer tissues. This is the largest verification study of biomarker candidate membrane proteins to date; our methods for biomarker discovery and subsequent validation using SRM/MRM will contribute to the identification of useful biomarker candidates for various cancers. Data are available via ProteomeXchange with identifier PXD000851.

Indexed as

ProteomicsBiomarkers, TumorColorectal NeoplasmsGene Expression Regulation, NeoplasticHumansMembrane ProteinsNeoplasm ProteinsTissue Array AnalysisBiomarkers, TumorMembrane ProteinsNeoplasm Proteins

Identifiers

PMID24687888
PMCPMC4047467
OpenAlexW2112279992

What OpenQuestion holds

Textmetadata
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.