Genome-Scale Discovery of DNA-Methylation Biomarkers for Blood-Based Detection of Colorectal Cancer

Background

There is an increasing demand for accurate biomarkers for early non-invasive colorectal cancer detection. We employed a genome-scale marker discovery method to identify and verify candidate DNA methylation biomarkers for blood-based detection of colorectal cancer.

Methodology/Principal Findings

We used DNA methylation data from 711 colorectal tumors, 53 matched adjacent-normal colonic tissue samples, 286 healthy blood samples and 4,201 tumor samples of 15 different cancer types. DNA methylation data were generated by the Illumina Infinium HumanMethylation27 and the HumanMethylation450 platforms, which determine the methylation status of 27,578 and 482,421 CpG sites respectively. We first performed a multistep marker selection to identify candidate markers with high methylation across all colorectal tumors while harboring low methylation in healthy samples and other cancer types. We then used pre-therapeutic plasma and serum samples from 107 colorectal cancer patients and 98 controls without colorectal cancer, confirmed by colonoscopy, to verify candidate markers. We selected two markers for further evaluation: methylated THBD (THBD-M) and methylated C9orf50 (C9orf50-M). When tested on clinical plasma and serum samples these markers outperformed carcinoembryonic antigen (CEA) serum measurement and resulted in a high sensitive and specific test performance for early colorectal cancer detection.

Conclusions/Significance

Our systematic marker discovery and verification study for blood-based DNA methylation markers resulted in two novel colorectal cancer biomarkers, THBD-M and C9orf50-M. THBD-M in particular showed promising performance in clinical samples, justifying its further optimization and clinical testing.     

A novel multiplexed immunoassay identifies CEA,IL-8 and prolactin as prospective markers for Dukes’ stages A-D colorectal cancers

Background

Current methods widely deployed for colorectal cancers (CRC) screening lack the necessary sensitivity and specificity required for population-based early disease detection. Cancer-specific protein biomarkers are thought to be produced either by the tumor itself or other tissues in response to the presence of cancers or associated conditions. Equally, known examples of cancer protein biomarkers (e.g., PSA, CA125, CA19-9, CEA, AFP) are frequently found in plasma at very low concentration (pg/mL-ng/mL). New sensitive and specific assays are therefore urgently required to detect the disease at an early stage when prognosis is good following surgical resection. This study was designed to meet the longstanding unmet clinical need for earlier CRC detection by measuring plasma candidate biomarkers of cancer onset and progression in a clinical stage-specific manner. EDTA plasma samples (1 μL) obtained from 75 patients with Dukes’ staged CRC or unaffected controls (age and sex matched with stringent inclusion/exclusion criteria) were assayed for expression of 92 human proteins employing the Proseek® Multiplex Oncology I proximity extension assay. An identical set of plasma samples were analyzed utilizing the Bio-Plex Pro™ human cytokine 27-plex immunoassay.

Results

Similar quantitative expression patterns for 13 plasma antigens common to both platforms endorsed the potential efficacy of Proseek as an immune-based multiplex assay for proteomic biomarker research. Proseek found that expression of Carcinoembryonic Antigen (CEA), IL-8 and prolactin are significantly correlated with CRC stage.

Conclusions

CEA, IL-8 and prolactin expression were found to identify between control (unaffected), non-malignant (Dukes’ A + B) and malignant (Dukes’ C + D) stages.

Electronic supplementary material

The online version of this article (doi:10.1186/s12014-015-9081-x) contains supplementary material, which is available to authorized users.     

Serum methylation levels of TAC1. SEPT9 and EYA4 as diagnostic markers for early colorectal cancers: a pilot study

Abstract

Objective: To identify methylated genes in serum with diagnostic potentials for early colorectal cancer (CRC).

Methods: Serum methylation levels of up to 12 genes were measured in two sets of serum samples with the second set from 26 stage I CRC patients and 26 age/gender-matched controls.

Results: Serum methylation levels of TAC1, SEPT9, and EYA4 were significant discriminants between stage I CRC and healthy controls. Combination of TAC1 and SEPT9 rendered 73.1% sensitivity with 92.3% specificity.

Conclusion: Serum methylation levels of TAC1. SEPT9 and EYA4 may be useful biomarkers for early detection of CRC though a validation study is necessary.     

Colorectal adenoma and cancer detection based on altered methylation pattern of SFRP1, SFRP2, SDC2, and PRIMA1 in plasma samples

Aberrant methylation is one of the most frequent epigenetic alterations that can contribute to tumor formation. Cell-free DNA can originate from tumor tissue; therefore, the evaluation of methylation markers in cell-free DNA can be a promising method for cancer screening. Our aim was to develop a panel of biomarkers with altered methylation along the colorectal adenoma-carcinoma sequence in both colonic tissue and plasma. Methylation of selected CpG sites in healthy colonic (n = 15), adenoma (n = 15), and colorectal cancer (n = 15) tissues was analyzed by pyrosequencing. MethyLight PCR was applied to study the DNA methylation of SFRP1, SFRP2, SDC2, and PRIMA1 gene promoters in 121 plasma and 32 biopsy samples. The effect of altered promoter methylation on protein expression was examined by immunohistochemistry. Significantly higher (P < 0.05) DNA methylation levels were detected in the promoter regions of all 4 markers, both in CRC and adenoma tissues compared with healthy controls. Methylation of SFRP1, SFRP2, SDC2, and PRIMA1 promoter sequences was observed in 85.1%, 72.3%, 89.4%, and 80.9% of plasma samples from patients with CRC and 89.2%, 83.8%, 81.1% and 70.3% from adenoma patients, respectively. When applied as a panel, CRC patients could be distinguished from controls with 91.5% sensitivity and 97.3% specificity [area under the curve (AUC) = 0.978], while adenoma samples could be differentiated with 89.2% sensitivity and 86.5% specificity (AUC = 0.937). Immunohistochemical analysis indicated decreasing protein levels of all 4 markers along the colorectal adenoma-carcinoma sequence. Our findings suggest that this methylation biomarker panel allows non-invasive detection of colorectal adenoma and cancer from plasma samples.     

Plasma Protein Profiling Reveal Osteoprotegerin as a Marker of Prognostic Impact for Colorectal Cancer

BACKGROUND: Due to difficulties in predicting recurrences in colorectal cancer stages II and III, reliable prognostic biomarkers could be a breakthrough for individualized treatment and follow-up. OBJECTIVE: To find potential prognostic protein biomarkers in colorectal cancer, using the proximity extension assays. METHODS: A panel of 92 oncology-related proteins was analyzed with proximity extension assays, in plasma from a cohort of 261 colorectal cancer patients with stage II-IV. The survival analyses were corrected for disease stage and age, and the recurrence analyses were corrected for disease stage. The significance threshold was adjusted for multiple comparisons. RESULTS: The plasma proteins expression levels had a greater prognostic relevance in disease stage III colorectal cancer than in disease stage II, and for overall survival than for time to recurrence. Osteoprotegerin was the only biomarker candidate in the protein panel that had a statistical significant association with overall survival (P = .00029). None of the proteins were statistically significantly associated with time to recurrence. CONCLUSIONS: Of the 92 analyzed plasma proteins, osteoprotegerin showed the strongest prognostic impact in patients with colorectal cancer, and therefore osteoprotegerin is a potential predictive marker, and it also could be a target for treatments.     

A pilot study of circulating miRNAs as potential biomarkers of early stage breast cancer

Background

To date, there are no highly sensitive and specific minimally invasive biomarkers for detection of breast cancer at an early stage. The occurrence of circulating microRNAs (miRNAs) in blood components (including serum and plasma) has been repeatedly observed in cancer patients as well as healthy controls. Because of the significance of miRNA in carcinogenesis, circulating miRNAs in blood may be unique biomarkers for early and minimally invasive diagnosis of human cancers. The objective of this pilot study was to discover a panel of circulating miRNAs as potential novel breast cancer biomarkers.

Methodology/Principal Findings

Using microarray-based expression profiling followed by Real-Time quantitative Polymerase Cycle Reaction (RT-qPCR) validation, we compared the levels of circulating miRNAs in plasma samples from 20 women with early stage breast cancer (10 Caucasian American (CA) and 10 African American (AA)) and 20 matched healthy controls (10 CAs and 10 AAs). Using the significance level of p<0.05 constrained by at least two-fold expression change as selection criteria, we found that 31 miRNAs were differentially expressed in CA study subjects (17 up and 14 down) and 18 miRNAs were differentially expressed in AA study subjects (9 up and 9 down). Interestingly, only 2 differentially expressed miRNAs overlapped between CA and AA study subjects. Using receiver operational curve (ROC) analysis, we show that not only up-regulated but also down-regulated miRNAs can discriminate patients with breast cancer from healthy controls with reasonable sensitivity and specificity. To further explore the potential roles of these circulating miRNAs in breast carcinogenesis, we applied pathway-based bioinformatics exploratory analysis and predicted a number of significantly enriched pathways which are predicted to be regulated by these circulating miRNAs, most of which are involved in critical cell functions, cancer development and progression.

Conclusions

Our observations from this pilot study suggest that the altered levels of circulating miRNAs might have great potential to serve as novel, noninvasive biomarkers for early detection of breast cancer.     

Data fusion in metabolomic cancer diagnostics

We have recently shown that fluorescence spectroscopy of plasma samples has promising abilities regarding early detection of colorectal cancer. In the present paper, these results were further developed by combining fluorescence with the biomarkers, CEA and TIMP-1 and traditional metabolomic measurements in the form of ¹H NMR spectroscopy. The results indicate that using an extensive profile established by combining such measurements together with the biomarkers is better than using single markers.     

结直肠癌患者血浆甲基化Sept9基因的表达及临床意义

目的:探讨甲基化Sept9基因在结直肠癌患者血浆中的表达及临床意义。方法:选择2015年1月~2017年3月经陕西省人民医院病理证实的结直肠癌患者87例(结直肠癌组)、结直肠息肉患者79例(结直肠息肉组)、健康体检者93例(健康对照组)作为研究对象,采用实时荧光定量聚合酶链式反应(PCR)技术检测其外周血血浆Sept9基因甲基化情况,比较三组甲基化Sept9基因阳性表达率,分析甲基化Sept9基因阳性表达与结直肠癌病理特征的关系。结果:血浆甲基化Sept9基因在结直肠癌组、结直肠息肉组、健康对照组的阳性表达率分别为71.26%(62/87)、5.06%(4/79)、3.23%(3/93),差异有统计学意义(P0.05);血浆甲基化Sept9基因阳性表达与结直肠癌患者的性别、年龄、肿瘤部位、病理分型、血管侵犯、神经侵犯无关(P0.05),与肿瘤最大径、浸润深度、分化程度、淋巴结转移、TNM分期有关(P0.05);结直肠癌患者血浆甲基化Sept9基因阳性表达率为71.26%(62/87),高于血清CEA的54.02%(47/87)、CA199的35.63%(31/87)、CA724的33.33%(29/87)、CA125的21.84%(19/87),差异有统计学意义(P0.05)。结论:结直肠癌患者外周血血浆甲基化Sept9基因呈高表达状态,早期检测甲基化Sept9基因表达水平在结直肠癌的诊断及病情评估中有重要意义。     

Effect of aronia on thiol levels in plasma of breast cancer patients

The various specific biomarkers of oxidative stress in plasma from patients with breast cancer, as well as biomarkers (the level of lipid hydroperoxides, conjugated dienes, thiobarbituric acid reactive substances) have been described. The aim of our present study was to evaluate the amount of low-molecular-weight thiols (which are physiological free radical scavengers) and establish the effects of the extract from A. melanocarpa on the amount of these thiols in plasma obtained from patients with invasive breast cancer, patients with benign breast diseases and from healthy volunteers. We observed in patients the higher amounts of homocysteine in plasma from patients in comparison to plasma from the control group; however the total level of glutathione, cysteine, cysteinylglycine, and the amount of thiols in reduced and oxidized forms was changed (e.g., in patients, the decrease of glutathione and cysteine reached about 50% of total values). Moreover, we showed that in the presence of the extract of A. melanocarpa (50 μg/mL, 5 min, 37°C), changes in amount of thiols in plasma from patients with invasive breast cancer and patients with benign breast diseases were significantly reduced in vitro. Considering the data presented in this study, we suggest that the extract from A. melanocarpa has an effect on thiol metabolism and the levels of all tested thiols observed in plasma obtained from breast cancer patients.     

GJA1在结直肠癌组织中表达及促进侵袭转移的研究

摘要 目的：间隙连接Alpha-1蛋白（Gap Junction Alpha-1,GJA1）是间隙连接中分布最广泛的蛋白,并在多种肿瘤中起促癌作用,但其在结直肠癌发生、发展的作用研究甚少。本实验旨在探究GJA1在结直肠癌组织中的表达情况及其对结直肠癌细胞系侵袭、转移能力的影响,以期为结直肠癌的诊断和预后寻找新的生物标志物。方法：收集92对结直肠癌及其癌旁组织样本,提取组织RNA,利用qRT-PCR检测GJA1相对表达量,并分析GJA1表达与临床病理特征及预后的相关性。在HCT116和HCT8两种结直肠癌细胞系中分别构建GJA1过表达载体和敲减载体,利用qRT-PCR和、Western Blot检测上皮间充质转化（epithelial-mesenchymal transition, EMT）相关蛋白E-Cadherin、N-Cadherin、Vimentin和Snail的表达变化,利用Wound healing和Transwell实验观察其迁移、侵袭能力的变化。结果：相对于癌旁组织,GJA1在结直肠癌组织中显著低表达。并且结直肠癌中低表达的GJA1与肿瘤分化程度、浸润深度、淋巴血管转移相关,低表达GJA1结直肠癌患者显示更差的总体生存率和更低的无病生存率。此外,过表达GJA1后,结直肠癌细胞E-cadherin的表达升高,N-cadherin、Vimentin和Snail的表达降低,划痕愈合减慢,Transwell转移细胞减少;而敲减GJA1后,结直肠癌细胞E-Cadherin的表达降低,N-Cadherin、Vimentin和Snail的表达升高,划痕愈合加快,Transwell转移细胞增多。结论：GJA1在结直肠癌中低表达,其表达降低可通过EMT促进结直肠癌的侵袭、转移并影响病人预后。     

Plasma levels of resistin-like molecule beta in humans

Background: Resistin-like molecules (RELM) are expressed in many tissues and among those, RELMβ is most abundantly expressed in the colon. Based on animal studies, RELMβ is induced by high fat diets, obesity, and intestinal microflora and may play a role in insulin resistance and intestinal inflammation. In the present study, we evaluated whether RELMβ could be measured in human plasma and the influence of selected host and behavioral factors on RELMβ levels, including known risk factors for colorectal cancer. Methods: The subjects for this pilot study were derived from healthy controls who participated in a population-based case–control study of colorectal cancer in Metropolitan Detroit. The subjects were 45–80 years of age without history of cancer or colorectal resection. Results: RELMβ was present in human plasma, with levels in the range of 0.08–0.26 ng/mL. Lower RELMβ levels were found in subjects with non-Caucasian race, lower pack-years of smoking, and higher physical activity index scores. Other variables such as dietary intakes, gender, obesity, use of non-steroidal anti-inflammatory agents and history of polyps were not associated with RELMβ levels. Conclusions: The direct association of RELMβ with smoking and inverse association with physical activity, both of which are risk factors for colon cancer, indicates that RELMβ may be involved in mediating the effects of these two lifestyle factors on risk of colon cancer.     

Clinical significance of preoperative neutrophil-lymphocyte versus platelet-lymphocyte ratio in patients with operable colorectal cancer

The objective of this study was to clarify whether the neutrophil-lymphocyte ratio (NLR) and the platelet-lymphocyte ratio (PLR) are significant prognostic markers in patients with resectable colorectal cancer (CRC). A total of 200 patients who underwent curative resection for CRC were enrolled. The NLR and PLR were positively correlated (p?<?0.001). Both the NLR and PLR were shown to be good prognostic biomarkers of overall survival (OS) (p?=?0.002 and p?=?0.001, respectively). The PLR was an independent prognostic factor of OS based on multivariate analysis (hazard ratio, 1.971; 95% confidence interval, 1.102–3.335; p?=?0.021).     

Quantitative proteomics reveals differentially expressed proteins in murine preneoplastic intestine in a model of intestinal tumorigenesis induced by low dietary folate and MTHFR deficiency

Colorectal cancer risk is increased when dietary folate intake is low, with or without a deficiency in methylenetetrahydrofolate reductase (MTHFR). We have observed that intestinal tumors are induced in mice fed low‐folate diets, and that tumor incidence is increased when these mice also have MTHFR deficiency. This study was undertaken to identify differentially expressed proteins in conditions favoring initial steps of murine carcinogenesis in normal preneoplastic intestine. We compared the proteome of BALB/c normal intestine in Mthfr^+/+ mice fed control diets for 1 year (low susceptibility to tumorigenesis) with the proteome of Mthfr^+/? animals fed low folate diets (higher tumor susceptibility). Our data suggest that the NuRD complex, KRAS‐related proteins, the protein synthetic machinery, and fatty acid‐related metabolic proteins are upregulated in the early stages of tumorigenesis. These proteins may serve as biomarkers or targets for colorectal cancer diagnosis or therapy.     

Upregulation of plasma C9 protein in gastric cancer patients

Gastric cancer is one of the leading causes of cancer‐related deaths worldwide. Current biomarkers used in the clinic do not have sufficient sensitivity for gastric cancer detection. To discover new and better biomarkers, protein profiling on plasma samples from 25 normal, 15 early‐stage and 21 late‐stage cancer was performed using an iTRAQ‐LC‐MS/MS approach. The level of C9 protein was found to be significantly higher in gastric cancer compared with normal subjects. Immunoblotting data revealed a congruent trend with iTRAQ results. The discriminatory power of C9 between normal and cancer states was not due to inter‐patient variations and was independent from gastritis and Helicobacter pylori status of the patients. C9 overexpression could also be detected in a panel of gastric cancer cell lines and their conditioned media compared with normal cells, implying that higher C9 levels in plasma of cancer patients could be attributed to the presence of gastric tumor. A subsequent blind test study on a total of 119 plasma samples showed that the sensitivity of C9 could be as high as 90% at a specificity of 74%. Hence, C9 is a potentially useful biomarker for gastric cancer detection.     

Colorectal cancer and trace elements alteration

BackgroundTrace elements have important influence on body function primarily because of the vital role they have in many physiological processes. Their alterations have been found in many disorders, including cancer. It has been well known for decades that disturbances in elemental concentration may lead to cell damaging, DNA injuries and imbalance in oxidative burden. Our study tried to determine the difference of trace elements concentrations between colorectal adenocarcinoma and adjacent healthy intestinal tissue.Methods59 subjects participated in this study. Healthy colon mucosa samples and colon tumor tissue samples were obtained from patients previously diagnosed with colon carcinoma by standard diagnostic procedures. Analysis of the elements was performed by inductively coupled plasma mass spectrometry (ICP-MS).ResultsThe results showed that Na, K, Mg, Ca, Cu, Zn, Se, Mn, Cd, Cr and Hg significantly differ between malignant tissue of colorectal cancer (CRC) and adjacent healthy bowel tissue. We have, also, found that Cu/Zn tissue ratio was significantly higher in CRC compared to a healthy tissue and that patients with higher CRC stages had also significantly higher ratio.ConclusionsSince this is the first such study in Balkan region, we assume that results of our study could be a good indicator of elemental alterations in colorectal cancer of Balkan population, due to similarity in lifestyle, dietary intake, pollution and exposure to toxic elements.     

Effects of 5-Fluorouracil on Oxidative Stress and Calcium Levels in the Blood of Patients with Newly Diagnosed Colorectal Cancer

The administration of chemotherapeutic agents for colorectal carcinoma is associated with an increase in oxidative stress and a concomitant decrease in antioxidant and element levels in the blood. This study investigated the effects of 5-fluorouracil (5-FU) chemotherapy on the levels of lipid peroxidation, reduced glutathione (GSH), glutathione peroxidase (GSH-Px), antioxidant vitamins, and elements in colorectal cancer patients. Twelve patients with newly diagnosed colorectal carcinoma and 12 healthy subjects were included in this study. Blood samples were collected from both the healthy controls and patients. 5-FU was intravenously administered to the patients for 6 weeks, and blood samples were collected again from the treatment group. In the patient group, lipid peroxidation levels were increased in both the plasma and erythrocyte samples, whereas GSH-Px activity and concentrations of GSH, vitamin E, and β-carotene in erythrocytes were decreased. The oxidant, antioxidant, and plasma calcium values were lower in 5-FU-treated patients than in the controls. Plasma vitamin A, chloride, sodium, and potassium concentrations did not change with 5-FU treatment. In conclusion, oxidative stress in patients with newly diagnosed colorectal cancer is attributable to the disease and not to 5-FU treatment. Blood vitamin E, β-carotene, GSH, and GSH-Px levels could be useful as early biomarkers of the prognosis of colorectal cancer patients.     

Expression analysis of circulating plasma long noncoding RNAs in colorectal cancer: The relevance of lncRNAs ATB and CCAT1 as potential clinical hallmarks

Long noncoding RNAs (lncRNAs) have been demonstrated to regulate a variety of cell processes and involve in the development and progression of colorectal cancer (CRC). Recently, the circulating lncRNAs have emerged as minimally invasive biomarkers for cancer diagnosis and prognosis. We aimed to examine the plasma expression level of long noncoding RNAs lnc-ATB, lnc-CCAT1, and lnc-OCC-1 in CRC patients and evaluate the clinical values. A total of 74 pretreatment CRC and 74 healthy blood biopsies were subjected to differentially evaluate the expression levels of three lncRNAs (OCC-1, CCAT1, and ATB). Briefly, after plasma separation and total RNA extraction, RNAs were reversely transcribed to complementary DNA followed by amplification using a quantitative real-time polymerase chain reaction technique for lncRNA expression analysis. The results showed that the expression levels of lnc-ATB (p < 0.001) and CCAT1 (p = 0.024), but not OCC-1 (p = 0.24), were significantly upregulated in the CRC compared with the healthy group. The calculated AUC of ROC was 0.78 (95% confidence interval [CI]: 0.811–0.94) for lnc-ATB and 0.64 (95% CI: 0.811–0.94) for CCAT1, which were indicative of a high discriminatory power (p < 0.001). The highest accuracy for lncRNA-ATB was obtained at a cutoff point of 2.5, which corresponded to sensitivity and specificity of 82% and 75%, respectively. Our results suggested a significant accuracy of lncRNA-ATB and lncRNA-CCAT1 in distinguishing CRC patients from healthy individuals.     

Expression of p27Kip1 and bcl-2, cigarette smoking,and colorectal cancer risk

Although a positive association between cigarette smoking and colorectal adenoma development is consistently found, the association with colorectal cancer remains controversial. We evaluated the potential roles of p27^Kip1 and bcl-2 protein expressions in conjunction with cigarette smoking exposure and colorectal cancer risk in a hospital-based case-control study. A total of 163 colorectal cancer patients from Roswell Park Cancer Institute and Buffalo General Hospital and 326 healthy controls responded to a standardized questionnaire on colorectal cancer risk factors including detailed information on their history of cigarette smoking; 110 of the patients' tumours were available for immunohistochemical analysis of p27^Kip1 and bcl-2 protein overexpression. An avidin-biotin immunoperoxidase procedure was used to determine expression after incubation with mouse monoclonal p27^Kip1 and mouse monoclonal bcl-2 antibodies, respectively. A statistically significant trend for total pack-years of smoking was found when p27^Kip1 positive cases were compared with p27^Kip1 negative cases (trend test, p = 0.007). Although a weak inverse association was observed with smoking exposure among p27^Kip1 negative tumour cases in comparison to controls, a significant dose-response association was seen with p27^Kip1 positive tumours. The relative risk of developing a p27^Kip1 positive tumour was estimated to be 1.17 (95% CI 0.54-2.54) for those with less than 20 pack-years, 1.95 (95 % CI 0.95-3.97) for those with 20-39 pack-years, and 2.25 (95% CI 1.14-4.45) for those with greater than 39 pack-years of smoking exposure (trend test, p = 0.009) when compared with controls. When cases with bcl-2 expression were compared with cases without bcl-2 expression, suggestion of a trend was also observed with pack-years smoked (trend test, p = 0.09). In our study of 110 patients with sporadic colorectal cancer and 326 controls, we observed differences in associations between cigarette smoking and expressions in p27^Kip1 and bcl-2. Our data suggest that bcl-2 overexpression (or a bcl-2 dependent pathway) is associated with cigarette smoking in the development of colorectal cancer, whereas a loss of p27^Kip1 expression is not. These associations indicate that there is aetiological heterogeneity in colorectal cancer development, and that they can indirectly allude to where these changes in protein expression occur in the adenoma-carcinoma sequence (i.e. early versus late events).