In-depth proteomic delineation of the colorectal cancer exoproteome: Mechanistic insight and identification of potential biomarkers

Karagiannis, George S.; Pavlou, Maria; Saraon, Punit; Musrap, Natasha; Xie, Annie; Batruch, Ihor; Prassas, Ioannis; Dimitromanolakis, Apostolos; Petraki, Constantina; Diamandis, Eleftherios P.

doi:10.1016/j.jprot.2014.03.018

Cited by 24 publications

(18 citation statements)

References 126 publications

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“…To address this issue, we deployed a three-step analytic procedure based on predictions from classical (Signal P) or non-classical (Secretome P) protein secretion and the presence of transmembrane helices (TMHMM). Then, we categorized all proteins into four categories depending on the scores that each protein received throughout the procedure (Supplemental Figure S2A) [43, 44]. The 1156 proteins were divided into the following groups: classical secretome proteins (Part 4), extracellular membrane proteins (Part 3), non-classical secretome proteins (Part 1) or other proteins (Part 2) (Supplemental Figure S2A&B).…”

Section: Resultsmentioning

confidence: 99%

“…This analysis resulted in the significant ( p <0.05) over-representation of 692 GO terms (Supplemental Table S6). Because several annotations are branched together, we visualized the analysis as an enrichment network, which algorithmically clustered GO terms with highly similar content using the enrichment map plug-in in the Cytoscape environment [44, 50-52]. A higher significance level (Benjamini & Hochberg corrected p-value < 1×10 −7 ) was selected for our next analysis.…”

Section: Resultsmentioning

confidence: 99%

“…To address the large-scale N-glycosecretome data, an underscored reproducible and biologically relevant criteria for candidate selection were used [56, 57]. As a proof-of-concept, here, we will exclusively focus on the “cell adhesion” clusters of the enrichment map because of its high significance and confidence (Benjamini & Hochberg corrected p- value =4.62×10-44).…”

Section: Resultsmentioning

confidence: 99%

“…The following cutoffs were considered a successful pass: 0.5 for SecretomeP (>0.5 or ≤ 0.5) and a 0 score for TMHMM (=0 or ≠0). An automation tool was developed in-house in Perl and can be run on a Windows Perl environment, facilitating the mapping of a list of protein identities to sequences, running the three prediction software programs mentioned above and creating a report file with consolidated predictions [44]. …”

Section: Methodsmentioning

confidence: 99%

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In-depth analysis of secretome and N-glycosecretome of human hepatocellular carcinoma metastatic cell lines shed light on metastasis correlated proteins

Jiang

Zhao

et al. 2016

Oncotarget

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Cancer cell metastasis is a major cause of cancer fatality. But the underlying molecular mechanisms remain incompletely understood, which results in the lack of efficient diagnosis, therapy and prevention approaches. Here, we report a systematic study on the secretory proteins (secretome) and secretory N-glycoproteins (N-glycosecretome) of four human hepatocellular carcinoma (HCC) cell lines with different metastatic potential, to explore the molecular mechanism of metastasis and supply the clues for effective measurement of diagnosis and therapy. Totally, 6242 unique gene products (GPs) and 1637 unique N-glycosites from 635 GPs were confidently identified. About 4000 GPs on average were quantified in each of the cell lines, 1156 of which show differential expression (p<0.05). Ninety-nine percentage of the significantly altered proteins were secretory proteins and proteins correlated to cell movement were significantly activated with the increasing of metastatic potential of the cell lines. Twenty-three GPs increased both in the secretome and the N-glycosecretome were chosen as candidates and verified by western blot analysis, and 10 of them were chosen for immunohistochemistry (IHC) analysis. The cumulative survival rates of the patients with candidate (FAT1, DKK3) suggested that these proteins might be used as biomarkers for HCC diagnosis. In addition, a comparative analysis with the published core human plasma database (1754 GPs) revealed that there were 182 proteins not presented in the human plasma database but identified by our studies, some of which were selected and verified successfully by western blotting in human plasma.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

In-depth analysis of secretome and N-glycosecretome of human hepatocellular carcinoma metastatic cell lines shed light on metastasis correlated proteins

Jiang

Zhao

et al. 2016

Oncotarget

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“…Nevertheless it is a prototype that encourages the search for a fuller understanding of the mechanism of action of ATRA in successful treatment regimens so that combination therapy with ATRA can be extended to other cancer types. However, for colorectal [67, 68], endometrial adenocarcinoma [69], solid gastric, pancreatic, head and neck [68] cancers, high level of OLFM4 is a negative prognostic factor. For prostate cancer, the deletion of OLFM4 gene was reported to be associated with tumor progression [70].…”

Section: Retinoids In Treatment and Chemopreventionmentioning

confidence: 99%

Retinoid Chemoprevention: Who Can Benefit?

Bunaciu

Yen

2015

Curr Pharmacol Rep

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Acute promyelocytic leukemia (APL) is a treatment success story. From a highly deadly disease it was turned into a highly curable disease by the introduction of differentiation-induction therapy with all-trans retinoic acid (ATRA) in the 1990's. During the last quarter of century, ATRA and other retinoids were used for the treatment and prevention of other cancers and even other diseases. The results were less spectacular, but nevertheless important. Progress has been made toward understanding the mechanism of action of retinoids in different physiological and pathological contexts. For some diseases, specific genetic backgrounds were found to confer responsiveness to retinoid therapy. Therapies that include retinoids and other modalities are very diverse and used both for combined targeting of multiple pathways and for diminishing toxicity.

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Olfactomedin‐4 is a candidate biomarker of solid gastric, colorectal, pancreatic, head and neck, and prostate cancers

Guette

Valo

Vétillard

et al. 2014

Proteomics Clinical Apps

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Olfactomedin-4 (OLFM4, OLM4) is a 72 kDa secreted glycoprotein belonging to the olfactomedin family. The OLFM4 gene expression is regulated by the transcription factors NF-kappa B and AP-1, and the OLM4 functions are poorly understood. OLM4 has been described as being able to interact with cell surface proteins such as lectins and concanavalin-A suggesting that one function of OLM4 is to regulate cell adhesion and migration. OLM4 is a marker for intestinal stem cells and is expressed at the bottom of the intestinal crypts. Expression of OLM4 during tumor development showed that OLM4 expression is increased in the early stages of tumor initiation. As OLM4 is a secreted protein, it is a prime candidate for biomarker research for tumor detection or progression. Levels of circulating OLM4 were significantly higher in patients with gastric, colorectal, and pancreatic cancers than in healthy subjects.

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In-depth proteomic delineation of the colorectal cancer exoproteome: Mechanistic insight and identification of potential biomarkers

Cited by 24 publications

References 126 publications

In-depth analysis of secretome and N-glycosecretome of human hepatocellular carcinoma metastatic cell lines shed light on metastasis correlated proteins

In-depth analysis of secretome and N-glycosecretome of human hepatocellular carcinoma metastatic cell lines shed light on metastasis correlated proteins

Retinoid Chemoprevention: Who Can Benefit?

Olfactomedin‐4 is a candidate biomarker of solid gastric, colorectal, pancreatic, head and neck, and prostate cancers

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