Functional protease profiling with reporter peptides in serum specimens of colorectal cancer patients: demonstration of its routine diagnostic applicability

Peptide probes for proteases - innovations and applications for monitoring proteolytic activity

Proteases are excellent biomarkers for a variety of diseases, offer multiple opportunities for diagnostic applications and are valuable targets for therapy. From a chemistry-based perspective this review discusses and critiques the most recent advances in the field of substrate-based probes for the detection and analysis of proteolytic activity both in vitro and in vivo.

Mining the Human Proteome: Biomarker Discovery for Human Cancer and Metastases

As our knowledge of the mechanisms underlying cancer development and progression has increased, so too have more effective, less toxic, and targeted therapies begun to reach the clinic. However, the full impact of these clinical advances and the practical success of the emerging field of precision medicine are dependent on the discovery and validation of sensitive and accurate biomarkers that can enable appropriate and rigorous sample type and patient selection, reliable longitudinal monitoring of therapeutic efficacy, and even risk assessment and early detection. Within the context of this review, we examine state-of-the-art approaches to the discovery and validation of noninvasive cancer biomarkers, with a specific emphasis on those that are protein or protein-associated ones. We also review sample selection strategies, currently utilized proteomic approaches for both discovery and validation requirements, and data analysis standards. Finally, we provide examples of these elements of biomarker discovery and validation from our own biomarker research.

Alterations of the Plasma Peptidome Profiling in Colorectal Cancer Progression

Early detection of colorectal cancer (CRC) remains a challenge. It has been highlighted that the pathological alterations within an organ and tissues might be reflected in serum or plasma proteomic/peptidic patterns. The aim of the study was to follow the changes in the plasma peptides associated to colorectal cancer progression by mass spectrometry. This study included 27 adenoma, 67 CRC (n = 33 I-II stage and n = 34 III-IV stage), 23 liver metastasis from CRC patients and 34 subjects disease-free as controls. For plasma peptides analysis, samples purification was performed on the Nanoporous Silica Chips technology followed by matrix-assisted laser desorption/ionisation-time of flight analysis. Since the high complexity of the obtained dataset, multivariate statistical analysis, and discriminant pattern recognition were performed for study groups classification. Forty-four of 88 ionic species were successfully identified as fragments of peptides and proteins physiologically circulating in the blood and belonging to immune and coagulation systems and inflammatory mediators. Many peptides clustered into sets of overlapping sequences with ladder-like truncation clearly associated to proteolytic processes of both endo- and exoproteases activity. Comparing to controls, a different median ion intensity of the group-type fragments distribution was observed. Moreover, the degradation pattern obtained by proteolytic cleavage was different into study groups. This pattern was specific and characteristic of each group: controls, colon tumour disease (including adenoma and CRC), and liver metastasis, revealing a role as biomarker in early diagnosis and prognosis. Our findings highlighted peculiar changes in protease activity characteristic of CRC progression from pre-cancer lesion to metastatic disease. J. Cell. Physiol. 231: 915-925, 2016. © 2015 Wiley Periodicals, Inc.

Association between NQO1 C609T polymorphism and prostate cancer risk

Published studies on the association between NQO1 C609T polymorphism and prostate cancer risk have yielded conflicting results. Thus, a systemic review and meta-analysis of published studies were performed to assess the possible association. All eligible studies of NQO1 C609T polymorphism and prostate cancer risk were collected from the PubMed and the Cochrane Library. Statistical analyses were performed by Review Manage 5.0 and Stata 11.0. A total of 6 available studies were considered in the present meta-analysis, with 717 cases and 1,794 controls. When all groups were pooled, there was no evidence that NQO1 C609T had significant association with prostate cancer under additive, recessive, dominant, and allelic models. When stratifying for the race, our analysis suggested that NQO1 C609T was associated with prostate cancer risk in Asians when using dominant (TT + CT vs CC: OR = 1.419, 95 % CI = 1.053 - 1.913, P = 0.021) and allelic models (OR = 1.337, 95 % CI = 1.014 - 1.763, P = 0.040) to analyze the data. However, no significant associations were found in Caucasians. This meta-analysis suggested that NQO1 C609T polymorphism most likely contributes to increased susceptibility to prostate cancer in the Asians. Further large-scale and well-designed case-control studies are necessary to validate the risk identified in the present meta-analysis.

Multiplex profiling of tumor-associated proteolytic activity in serum of colorectal cancer patients

PURPOSE

The monitoring of tumor-associated protease activity in blood specimens has recently been proposed as new diagnostic tool in cancer research. In this paper, we describe the screening of a peptide library for identification of reporter peptides (RPs) that are selectively cleaved in serum specimens from colorectal cancer patients and investigate the benefits of RP multiplexing.

EXPERIMENTAL DESIGN

A library of 144 RPs was constructed that contained amino acid sequences of abundant plasma proteins. Proteolytic cleavage of RPs was monitored with MS. Five RPs that were selectively cleaved in serum specimens from tumor patients were selected for further validation in serum specimens of colorectal tumor patients (n = 30) and nonmalignant controls (n = 60).

RESULTS

RP spiking and subsequent quantification of proteolytic fragments with LC-MS showed good reproducibility with CVs always below 26%. The linear discriminant analysis and PCA revealed that a combination of RPs for diagnostic classification is superior to single markers. Classification accuracy reached 88% (79/90) when all five markers were combined.

CONCLUSIONS AND CLINICAL RELEVANCE

Functional protease profiling with RPs might improve the laboratory-based diagnosis, monitoring and prognosis of malignant disease, and has to be evaluated thoroughly in future studies.

Association between IRS-1 Gly972Arg polymorphism and colorectal cancer risk

In order to make a comprehensive assessment of the potential association between one genetic variant in the insulin receptor substrate 1 (IRS-1) gene, rs1801278, and colorectal cancer (CRC) risk, we conducted a meta-analysis of four epidemiological studies, which included 3,708 CRC cases and 4,176 controls. The data showed that rs1801278 polymorphism was not associated with increased CRC risk in the overall population. When stratifying by the race, the results showed that the rs1801278 polymorphism was associated with increased CRC risk under dominant model in mixed populations. Based on this meta-analysis, we conclude that the IRS-1 rs1801278 polymorphism might be a risk factor for CRC development in mixed populations. Further studies, either with larger sample size or involving other single nucleotide polymorphisms (SNPs) and haplotypes of the IRS-1 gene, are necessary to clarify the contribution of IRS-1 rs1801278 in colorectal carcinogenesis.

Association between estrogen receptor alpha PvuII polymorphism and prostate cancer risk

Accumulating evidence has suggested that estrogen receptor alpha (ER-α) PvuII polymorphism might be involved in the development of prostate cancer (PCa). However, the results have been inconsistent. We therefore performed a meta-analysis to clarify the associations between ER-α PvuII polymorphism and PCa. A comprehensive search was conducted to identify all case-control studies of ER-α PvuII polymorphism and PCa risk. We used odds ratios (ORs) to assess the strength of the association and 95% confidence intervals (CIs) to give a sense of the precision of the estimate. A total of 14 studies were found to be eligible for meta-analyses of PvuII variant. Results from this study showed that ER-α PvuII polymorphism were significantly associated with PCa risk under all genetic models in overall population (homogeneous codominant model, OR = 1.57, 95% CI = 1.11-2.21, P = 0.010; heterogeneous codominant model, OR = 1.37, 95% CI = 1.06-1.77, P = 0.02; recessive model, OR = 1.27, 95% CI = 1.02-1.57, P = 0.03; dominant model, OR = 1.40, 95% CI = 1.09-1.79, P = 0.009; and allelic model, OR = 1.25, 95% CI = 1.06-1.48, P = 0.010). Further sensitivity analysis confirmed the significant association. In subgroup analyses stratified by PCa type, there was a significant association between PvuII polymorphism and sporadic PCa risk under both Caucasians and Asians. The meta-analysis indicated elected PvuII polymorphism of ER-α was a risk factor for PCa development.

Lack of association between interleukin-4 -524C>T polymorphism and colorectal cancer susceptibility

Interleukin-4 (IL-4) -524C > T polymorphism has been implicated to alter the risk of colorectal cancer (CRC), but the results are controversial. The objective of this study was to quantitatively evaluate the association between IL-4 -524C > T polymorphism and CRC risk. A comprehensive search was conducted to identify all eligible studies of IL-4 -524C > T polymorphism and CRC risk. Statistical analysis was performed with Review Manager 5.0 and Stata 11. A total of 5 case-control studies, including 1,224 cases and 1,551 controls, were included. The combined results based on all eligible studies suggested that IL-4 -524C > T polymorphism was not associated with CRC susceptibility. When stratifying for race, the data showed that the IL-4 -524C > T polymorphism was also not associated with an increased CRC susceptibility in Caucasians. Our study suggests that IL-4 -524C > T polymorphism may be not associated with an increased CRC susceptibility.

Association between IL-4 -589C>T polymorphism and colorectal cancer risk

In order to make a comprehensive assessment of the potential association between interleukin-4 (IL-4) -589C>T and colorectal cancer (CRC) susceptibility, we conducted a meta-analysis of six epidemiological studies, which included 1,317 CRC patients and 1,659 controls. The data showed that IL-4 -589C>T was not associated with increased CRC risk in the overall population. In the subgroup analysis of IL-4 -589C>T, the results did not change when the analyses were restricted to race. Based on this meta-analysis, we conclude that IL-4 -589C>T may be not a risk factor for CRC development. Further research is needed to assess possible gene-gene or gene-environment-lifestyle interactions on CRC.