Mass spectrometry-assisted gel-based proteomics in cancer biomarker discovery: approaches and application

Huang, Rongrong; Chen, Zhongsi; He, Lei; He, Nongyue; Zhang, Xi; Li, Zhiyang; Deng, Yan; Zeng, Xin

doi:10.7150/thno.20797

Cited by 62 publications

(35 citation statements)

References 218 publications

(220 reference statements)

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“…Prostate cancer is one of the most common malignancies among men, with a global incidence of 1.3 million new cases every year [ 199 ]. While prostate cancer may require minimal or even no treatment at early stages, metastasizing to the bone is a serious concern for about 65–80% of advanced stage cases [ 200 , 201 ]. The five-year survival rate of prostate cancer patients with localized prostate cancer has increased to over 90% with improved technologies for the treatment at an early stage; however, once the tumor cells metastasize, the 5-year survival rate substantially decreases to only 28% [ 202 ].…”

Section: Clinical Serum/plasma Proteomics and Molecular Signaturesmentioning

confidence: 99%

Challenges and Opportunities in Clinical Applications of Blood-Based Proteomics in Cancer

Bhawal

Oberg

Zhang

et al. 2020

Cancers

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Blood is a readily accessible biofluid containing a plethora of important proteins, nucleic acids, and metabolites that can be used as clinical diagnostic tools in diseases, including cancer. Like the on-going efforts for cancer biomarker discovery using the liquid biopsy detection of circulating cell-free and cell-based tumor nucleic acids, the circulatory proteome has been underexplored for clinical cancer biomarker applications. A comprehensive proteome analysis of human serum/plasma with high-quality data and compelling interpretation can potentially provide opportunities for understanding disease mechanisms, although several challenges will have to be met. Serum/plasma proteome biomarkers are present in very low abundance, and there is high complexity involved due to the heterogeneity of cancers, for which there is a compelling need to develop sensitive and specific proteomic technologies and analytical platforms. To date, liquid chromatography mass spectrometry (LC-MS)-based quantitative proteomics has been a dominant analytical workflow to discover new potential cancer biomarkers in serum/plasma. This review will summarize the opportunities of serum proteomics for clinical applications; the challenges in the discovery of novel biomarkers in serum/plasma; and current proteomic strategies in cancer research for the application of serum/plasma proteomics for clinical prognostic, predictive, and diagnostic applications, as well as for monitoring minimal residual disease after treatments. We will highlight some of the recent advances in MS-based proteomics technologies with appropriate sample collection, processing uniformity, study design, and data analysis, focusing on how these integrated workflows can identify novel potential cancer biomarkers for clinical applications.

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Section: Clinical Serum/plasma Proteomics and Molecular Signaturesmentioning

confidence: 99%

Challenges and Opportunities in Clinical Applications of Blood-Based Proteomics in Cancer

Bhawal

Oberg

Zhang

et al. 2020

Cancers

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“…During the following years, several milestones for MS in the clinics (for analytes other than proteins) were achieved such as tandem MS for newborn screening in 1990. The clinics may have been embracing the MS methodology slowly as discussed elsewhere 57 compared to the research community, which is now, more than ever, relying on MS data prior to concluding (several journals even require MS data to publish results for certain analytes 56 ). Even though several analytical platforms have previously been used for protein analyses, now the proteomic investigations are mostly carried out with MS and are divided into two main categories, targeted and non-targeted analysis.…”

Section: Mass Spectrometry In Protein Analysismentioning

confidence: 99%

Instant on-paper protein digestion during blood spot sampling

Skjærvø

Rosting

Halvorsen

et al. 2017

Analyst

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A concept integrating sampling and protein digestion is introduced here combining fast and simple fabrication by wax printing on filter paper with trypsin immobilized polymer beads. The paper reactors showed promising results with a high degree of protein digestion within fifty minutes in model protein mixtures as well as in human blood. The model protein mixture was used for the evaluation of performance both with and without a reduction and alkylation step. The paper reactors without reduction and alkylation showed between 46% and 75% protein sequence coverage and between five and 20 high confidence peptides (one and five zero missed cleavage peptides, respectively). Compared to a conventional in-solution approach, the paper reactor showed 10% less protein sequence coverage, 29% fewer high confidence peptides and 19% fewer high confidence peptides with zero missed cleavages. Placement of the protein reduction and alkylation step (before or after protein digestion) was shown to be of low importance. The storage stability of the paper reactors with (six weeks) and without (twelve weeks) tryptic peptides was satisfactory. The ability of the paper reactors to digest complex biological samples was investigated by comparison with human whole blood samples prepared using a conventional dried blood spot (DBS) procedure with overnight digestion in non-targeted analysis. The reactors showed a comparable performance with 75 ± 25 for the protein groups compared to 76 ± 5 for the DBS samples. Additionally, 267 ± 72 and 335 ± 11 unique peptides (high confidence) were identified for on-paper digestion and DBS, respectively.

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“…With the regulatory events often occurring at gene promoters, we speculated that some tumor-specific cellular factors might bind specifically to the CLC-3 promoter to upregulate CLC-3 expression. Therefore, an optimal promoter probe was synthesized to pull down CLC-3 promoter-binding proteins [ 32 , 33 ]. Our study demonstrated that XRCC5 bound the CLC-3 promoter, and increased combination was observed in GC cells, suggesting that this increased binding might be a promoting factor of CLC-3 overexpression.…”

Section: Discussionmentioning

confidence: 99%

Overexpression of CLC-3 is regulated by XRCC5 and is a poor prognostic biomarker for gastric cancer

Xiao-ya

et al. 2018

J Hematol Oncol

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BackgroundRecently, many potential prognostic biomarkers for gastric cancer (GC) have been identified, but the prognosis of advanced GC patients remains poor. Chloride channels are promising cancer biomarkers, and their family member chloride channel-3 (CLC-3) is involved in multiple biological behaviors. However, whether CLC-3 is a prognostic biomarker for GC patients is rarely reported. The molecular mechanisms by which CLC-3 is regulated in GC are unclear.MethodsThe expression of CLC-3 and XRCC5 in human specimens was analyzed using immunohistochemistry. The primary biological functions and pathways related to CLC-3 were enriched by RNA sequencing. A 5′-biotin-labeled DNA probe with a promoter region between − 248 and + 226 was synthesized to pull down CLC-3 promoter-binding proteins. Functional studies were detected by MTS, clone formation, wound scratch, transwell, and xenograft mice model. Mechanistic studies were investigated by streptavidin-agarose-mediated DNA pull-down, mass spectrometry, ChIP, dual-luciferase reporter assay system, Co-IP, and immunofluorescence.ResultsThe results showed that CLC-3 was overexpressed in human GC tissues and that overexpression of CLC-3 was a poor prognostic biomarker for GC patients (P = 0.012). Furthermore, higher expression of CLC-3 was correlated with deeper tumor invasion (P = 0.006) and increased lymph node metastasis (P = 0.016), and knockdown of CLC-3 inhibited cell proliferation and migration in vitro. In addition, X-ray repair cross-complementing 5 (XRCC5) was identified as a CLC-3 promoter-binding protein, and both CLC-3 (HR 1.671; 95% CI 1.012–2.758; P = 0.045) and XRCC5 (HR 1.795; 95% CI 1.076–2.994; P = 0.025) were prognostic factors of overall survival in GC patients. The in vitro and in vivo results showed that the expression and function of CLC-3 were inhibited after XRCC5 knockdown, and the inhibition effects were rescued by CLC-3 overexpression. Meanwhile, the expression and function of CLC-3 were promoted after XRCC5 overexpression, and the promotion effects were reversed by the CLC-3 knockdown. The mechanistic study revealed that knockdown of XRCC5 suppressed the binding of XRCC5 to the CLC-3 promoter and subsequent promoter activity, thus regulating CLC-3 expression at the transcriptional level by interacting with PARP1.ConclusionsOur findings indicate that overexpression of CLC-3 is regulated by XRCC5 and is a poor prognostic biomarker for gastric cancer. Double targeting CLC-3 and XRCC5 may provide the promising therapeutic potential for GC treatment.Electronic supplementary materialThe online version of this article (10.1186/s13045-018-0660-y) contains supplementary material, which is available to authorized users.

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Mass spectrometry-assisted gel-based proteomics in cancer biomarker discovery: approaches and application

Cited by 62 publications

References 218 publications

Challenges and Opportunities in Clinical Applications of Blood-Based Proteomics in Cancer

Challenges and Opportunities in Clinical Applications of Blood-Based Proteomics in Cancer

Instant on-paper protein digestion during blood spot sampling

Overexpression of CLC-3 is regulated by XRCC5 and is a poor prognostic biomarker for gastric cancer

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