Assessment of serum proteomics to detect large colon adenomas

Progress in the field of noninvasive diagnostics for colorectal cancer: a systematic review for the accuracy of blood-based biomarkers for detection of advanced pre-cancerous lesions

BACKGROUND

Early detection of pre-cancerous adenomas through screening can reduce colorectal cancer (CRC) incidence. Fecal immunochemical tests are commonly used, but have limited sensitivity for pre-cancerous lesions. Blood-based screening may improve test sensitivity. This systematic review and meta-analysis was conducted to evaluate the accuracy of blood-based biomarkers for detection of advanced pre-cancerous lesions.

RESEARCH DESIGN AND METHODS

We present the accuracy of blood-based biomarkers for the detection of advanced pre-cancerous lesions. EMBASE, Web of Science and PubMed databases were searched, with study populations limited to adults diagnosed with advanced pre-cancerous lesions at colonoscopy, who had a blood-based biomarker test analyzed with reports of sensitivity and specificity.

RESULTS

69 studies were identified, which assessed 133 unique biomarkers sets. The best performing test was a panel of 6 miRNAs, with a sensitivity of 95% and specificity of 90% for advanced pre-cancerous lesions. Only 6 biomarkers demonstrated sensitivity ≥ 50% and specificity ≥ 90% for the detection of advanced pre-cancerous lesions.

CONCLUSION

Many different blood-based biomarkers have been assessed for detection of advanced pre-cancerous lesions, but few have progressed beyond the discovery stage. While some biomarkers have reported high sensitivity and specificity, larger prospective studies in unbiased intended-use screening populations are required for validation.

Colorectal cancer biomarker discovery and validation using LC-MS/MS-based proteomics in blood: truth or dare?

Globally, colorectal cancer (CRC) is the third most common malignant neoplasm. However, highly sensitive, specific, noninvasive tests that allow CRC diagnosis at an early stage are still needed. As circulatory blood reflects the physiological status of an individual and/or the disease status for several disorders, efforts have been undertaken to identify candidate diagnostic CRC markers in plasma and serum. In this review, the challenges, bottlenecks and promising properties of mass spectrometry (MS)-based proteomics in blood are discussed. More specifically, important aspects in clinical design, sample retrieval, sample preparation, and MS analysis are presented. The recent developments in targeted MS approaches in plasma or serum are highlighted as well.

Biomarker Signature Discovery from Mass Spectrometry Data

Mass spectrometry based high throughput proteomics are used for protein analysis and clinical diagnosis. Many machine learning methods have been used to construct classifiers based on mass spectrometry data, for discrimination between cancer stages. However, the classifiers generated by machine learning such as SVM techniques typically lack biological interpretability. We present an innovative technique for automated discovery of signatures optimized to characterize various cancer stages. We validate our signature discovery algorithm on one new colorectal cancer MALDI-TOF data set, and two well-known ovarian cancer SELDI-TOF data sets. In all of these cases, our signature based classifiers performed either better or at least as well as four benchmark machine learning algorithms including SVM and KNN. Moreover, our optimized signatures automatically select smaller sets of key biomarkers than the black-boxes generated by machine learning, and are much easier to interpret.

Proteomic and cytokine plasma biomarkers for predicting progression from colorectal adenoma to carcinoma in human patients

In the present study, we screened proteomic and cytokine biomarkers between patients with adenomatous polyps and colorectal cancer (CRC) in order to improve our understanding of the molecular mechanisms behind turmorigenesis and tumor progression in CRC. To this end, we performed comparative proteomic analysis of plasma proteins using a combination of 2DE and MS as well as profiled differentially regulated cytokines and chemokines by multiplex bead analysis. Proteomic analysis identified 11 upregulated and 13 downregulated plasma proteins showing significantly different regulation patterns with diagnostic potential for predicting progression from adenoma to carcinoma. Some of these proteins have not previously been implicated in CRC, including upregulated leucine-rich α-2-glycoprotein, hemoglobin subunit β, Ig α-2 chain C region, and complement factor B as well as downregulated afamin, zinc-α-2-glycoprotein, vitronectin, and α-1-antichymotrypsin. In addition, plasma levels of three cytokines/chemokines, including interleukin-8, interferon gamma-induced protein 10, and tumor necrosis factor α, were remarkably elevated in patients with CRC compared to those with adenomatous polyps. Although further clinical validation is required, these proteins and cytokines can be established as novel biomarkers for CRC and/or its progression from colon adenoma.

Proteomics: methodologies and applications to the study of human diseases

Proteomic approach has allowed large-scale studies of protein expression in different tissues and body fluids in discrete conditions and/or time points. Recent advances of methodologies in this field have opened new opportunities to obtain relevant information on normal and abnormal processes occurring in the human body. In the current report, the main proteomics techniques and their application to human disease study are reviewed.

Elevated C-peptide and insulin predict increased risk of colorectal adenomas in normal mucosa

BACKGROUND

Lower concentrations of the insulin-like growth factor binding protein-1 (IGFBP-1) and elevated concentrations of insulin or C-peptide have been associated with an increase in colorectal cancer risk (CRC). However few studies have evaluated IGFBP-1 and C-peptide in relation to adenomatous polyps, the only known precursor for CRC.

METHODS

Between November 2001 and December 2002, we examined associations between circulating concentrations of insulin, C-peptide, IGFBP-1 and apoptosis among 190 individuals with one or more adenomatous polyps and 488 with no adenomatous polyps using logistic regression models.

RESULTS

Individuals with the highest concentrations of C-peptide were more likely to have adenomas (OR = 2.2, 95% CI 1.4-4.0) than those with the lowest concentrations; associations that appeared to be stronger in men (OR = 4.4, 95% CI 1.7-10.9) than women. Individuals with high insulin concentrations also had a higher risk of adenomas (OR = 3.5, 95% CI 1.7-7.4), whereas higher levels of IGFBP-1 were associated with a reduced risk of adenomas in men only (OR = 0.3, 95% CI 0.1-0.7). Overweight and obese individuals with higher C-peptide levels (>1(st) Q) were at increased risk for lower apoptosis index (OR = 2.5, 95% CI 0.9-7.1), an association that remained strong in overweight and obese men (OR = 6.3, 95% CI 1.0-36.7). Higher levels of IGFBP-1 in overweight and obese individuals were associated with a reduced risk of low apoptosis (OR = 0.3, 95% CI 0.1-1.0).

CONCLUSIONS

Associations between these peptides and the apoptosis index in overweight and obese individuals, suggest that the mechanism by which C-peptide could induce adenomas may include its anti-apoptotic properties. This study suggests that hyperinsulinemia and IGF hormones predict adenoma risk, and that outcomes associated with colorectal carcinogenesis maybe modified by gender.

Molecular tests for colorectal cancer screening

Detecting and removing high-risk adenomas and early colorectal cancer (CRC) can reduce mortality of this disease. The noninvasive fecal occult blood test (FOBT; guaiac-based or immunochemical) is widely used in screening programs and although effective, it leaves room for improvement in terms of test accuracy. Molecular tests are expected to be more sensitive, specific and informative than current detection tests, and are promising future tools for CRC screening. This review provides an overview of the performances of DNA, RNA, and protein markers for CRC detection in stool and blood. Most emphasis currently is on DNA and protein markers. Among DNA markers there is trend to move away from mutation markers in favor of methylation markers. The recent boost in proteomics research leads to many new candidate protein markers. Usually in small series, some markers show better performance than the present FOBT. Evaluation in large well-controlled randomized trials is the next step needed to take molecular markers for CRC screening to the next level and warrant implementation in a screening setting.

Mass spectrometry of peptides and proteins from human blood

It is difficult to convey the accelerating rate and growing importance of mass spectrometry applications to human blood proteins and peptides. Mass spectrometry can rapidly detect and identify the ionizable peptides from the proteins in a simple mixture and reveal many of their post-translational modifications. However, blood is a complex mixture that may contain many proteins first expressed in cells and tissues. The complete analysis of blood proteins is a daunting task that will rely on a wide range of disciplines from physics, chemistry, biochemistry, genetics, electromagnetic instrumentation, mathematics and computation. Therefore the comprehensive discovery and analysis of blood proteins will rank among the great technical challenges and require the cumulative sum of many of mankind's scientific achievements together. A variety of methods have been used to fractionate, analyze and identify proteins from blood, each yielding a small piece of the whole and throwing the great size of the task into sharp relief. The approaches attempted to date clearly indicate that enumerating the proteins and peptides of blood can be accomplished. There is no doubt that the mass spectrometry of blood will be crucial to the discovery and analysis of proteins, enzyme activities, and post-translational processes that underlay the mechanisms of disease. At present both discovery and quantification of proteins from blood are commonly reaching sensitivities of ∼1 ng/mL.

Sources of bias in specimens for research about molecular markers for cancer

Claims about the diagnostic or prognostic accuracy of markers often prove disappointing when "discrimination" found between cancers versus normals is due to bias, a systematic difference between compared groups. This article describes a framework to help simplify and organize current problems in marker research by focusing on the role of specimens as a source of bias in observational research and using that focus to address problems and improve reliability. The central idea is that the "fundamental comparison" in research about markers (ie, the comparison done to assess whether a marker discriminates) involves two distinct processes that are "connected" by specimens. If subject selection (first process) creates baseline inequality between groups being compared, then laboratory analysis of specimens (second process) may erroneously find positive results. Although both processes are important, subject selection more fundamentally influences the quality of marker research, because it can hardwire bias into all comparisons in a way that cannot be corrected by any refinement in laboratory analysis. An appreciation of the separateness of these two processes-and placing investigators with appropriate expertise in charge of each-may increase the reliability of research about cancer biomarkers.

Endoscopy, morphology, morphometry and molecular markers: predicting cancer risk in colorectal adenoma

The evaluation of short- and long-term risk for developing cancer in patients with colorectal adenomas is controversial. Good, reliable predictors of cancer risk in any adenoma are currently lacking and are limited to adenoma size, number and histologic type. In fact, the evaluation of any adenoma or precancer lesion (e.g., hyperplastic polyps, serrated adenoma or aberrant crypt foci) within the colorectum may be assessed by a number of techniques ranging from direct visualization through the endoscope, to microscopic assessment, and to evaluation at the molecular level. Emerging techniques may yield improved methods of adenoma risk-assessment in the near future. For one, newer endoscopy technologies include chromoendoscopy or endocytoscopy, which now render endoscopists able to resolve the surface and subsurface mucosa at cellular resolution in vivo and in real time - thus, bringing the microscope to the patient's bedside. This new era in endoscopic imaging is dubbed 'histoendoscopy'. Further, while traditional views of classifying protruding and sessile lesions include those of Haggitt, the sm-classification, the Japanese and the so-called Vienna classifications to evaluate neoplasia, the development of new molecular techniques may give way to new methods of classifying preneoplasia and precancerous lesions. This review discusses some pros and cons of risk evaluation technologies in the colorectal tract by endoscopy, microscopy, and quantitative and molecular features. The morphometry-based studies performed over the past decades for the quantitative assessment of cellular and nuclear features within adenomas have failed to yield results amenable for clinical translation and are unlikely to improve further and gain widespread use with current technology. Rather, emerging knowledge of pathway-specific markers through the outlining of a molecular classification will likely be the basis for improved detection and diagnosis. The emerging genomic and proteomic technologies allowing for noninvasive tests to detect (asymptomatic) cancer and neoplasia are discussed. Lastly, the importance of recognizing bias and pitfalls and the adherence to guidelines for biomarker research are addressed.

A method for assessing and maintaining the reproducibility of mass spectrometric analyses of complex samples

Direct injection mass spectrometric analysis of biological samples is potentially an attractive approach to the discovery of diagnostic patterns for specific pathophysiological conditions because of its speed and simplicity. Despite the possible benefits offered by such a method, its extensive application has been limited so far by several factors, including the inadequate reproducibility of the analytical results. We describe a method for monitoring and optimizing the performance of mass spectrometers used for biomarker discovery studies, based on the analysis of patterns of standardized spectral features. The method was successfully applied to maintaining spectral reproducibility during a multi-day analysis of hundreds of serum samples despite an ion source failure, which necessitated minor maintenance. The monitoring method allowed the early detection of that failure and the restoration of the spectral profiles after the system was restarted.

The current state of proteomics in GI oncology

Proteomics refers to the study of the entire set of proteins in a given cell or tissue. With the extensive development of protein separation, mass spectrometry, and bioinformatics technologies, clinical proteomics has shown its potential as a powerful approach for biomarker discovery, particularly in the area of oncology. More than 130 exploratory studies have defined candidate markers in serum, gastrointestinal (GI) fluids, or cancer tissue. In this article, we introduce the commonly adopted proteomic technologies and describe results of a comprehensive review of studies that have applied these technologies to GI oncology, with a particular emphasis on developments in the last 3 years. We discuss reasons why the more than 130 studies to date have had little discernible clinical impact, and we outline steps that may allow proteomics to realize its promise for early detection of disease, monitoring of disease recurrence, and identification of targets for individualized therapy.