Identification of Serum Biomarkers for Gastric Cancer Diagnosis Using a Human Proteome Microarray

We aimed to globally discover serum biomarkers for diagnosis of gastric cancer (GC). GC serum autoantibodies were discovered and validated using serum samples from independent patient cohorts encompassing 1,401 participants divided into three groups, i.e. healthy, GC patients, and GC-related disease group. To discover biomarkers for GC, the human proteome microarray was first applied to screen specific autoantibodies in a total of 87 serum samples from GC patients and healthy controls. Potential biomarkers were identified via a statistical analysis protocol. Targeted protein microarrays with only the potential biomarkers were constructed and used to validate the candidate biomarkers using 914 samples. To provide further validation, the abundance of autoantibodies specific to the biomarker candidates was analyzed using enzyme-linked immunosorbent assays. Receiver operating characteristic curves were generated to evaluate the diagnostic accuracy of the serum biomarkers. Finally, the efficacy of prognosis efficacy of the final four biomarkers was evaluated by analyzing the clinical records. The final panel of biomarkers consisting of COPS2, CTSF, NT5E, and TERF1 provides high diagnostic power, with 95% sensitivity and 92% specificity to differentiate GC patients from healthy individuals. Prognosis analysis showed that the panel could also serve as independent predictors of the overall GC patient survival. The panel of four serum biomarkers (COPS2, CTSF, NT5E, and TERF1) could serve as a noninvasive diagnostic index for GC, and the combination of them could potentially be used as a predictor of the overall GC survival rate.Gastric cancer (GC)¹ is the second leading cause of cancer-related deaths. A total of 952,000 new GC cases (6.8% of the total of the new cancer case) and 723,000 deaths (8.8% of the total new cancer case) occurred in 2012 (1). The highest mortality rates have been reported in East Asia, including China, Japan, and Korea (2–4), and ∼60% of new GC cases and deaths worldwide occur in this region. As GC has a 5-year survival rate of less than 15%, accurate diagnosis and prognostic assessment of patients are essential for optimizing therapeutic strategies, predicting the outcome of treatment, extending the survival period of patients, and potentially healing to reduce cancer mortality (5).A variety of serum antigen biomarkers has been used for GC diagnosis and prognosis, e.g. carcinoembryonic antigen, carbohydrate antibody 19-9 (CA19-9), carbohydrate antibody 72-4 (CA72-4), and carbohydrate antibody 50 (CA50); the protein levels of these antigens in serum are usually used as signatures indicating cancer risk. However, generally, these serum antigen biomarkers lack sufficient sensitivity and specificity (6–8).Autoantibodies against proteins that result from abnormal gene expression and gene mutation in patients with various tumors represent another type of serum biomarker (9–12). The corresponding antigens of the autoantibodies are usually recognized as tumor-specific antigens or tumor-associated antigens (13–16). There is particular interest in these autoantibodies due to the potential diagnostic and prognostic applications of the autoantibodies and their corresponding antigens. Indeed, there is a need to identify novel autoantibody-based biomarkers to improve the sensitivity and specificity for the diagnosis of GC.In this study, we used a human proteome microarray containing 16,368 proteins to discover and independently validate serum autoantibodies with potential for diagnosis and prognosis of GC in a set of 1,401 serum samples. The samples were from 537 GC patients, 550 healthy controls, and 314 individuals of GC-related diseases. Four autoantigen serum biomarkers, COP9 constitutive photomorphogenic homolog subunit 2 (COPS2), CTSF, ecto-5′-nucleotidase (NT5E), and telomeric repeat binding factor 1 (TERF1), were identified with a combined diagnostic sensitivity of 95% and specificity of 92%. Furthermore, our data suggested COPS2, CTSF, NT5E, and TERF1 could also serve as potential predictors for prognostic assessment.     

Identification of Kininogen-1 as a Serum Biomarker for the Early Detection of Advanced Colorectal Adenoma and Colorectal Cancer

Background

Serum markers represent potential tools for the detection of colorectal cancer (CRC). The aim of this study was to obtain proteomic expression profiles and identify serum markers for the early detection of CRC.

Methods

Proteomic profiles of serum samples collected from 35 healthy volunteers, 35 patients with advanced colorectal adenoma (ACA), and 40 patients with CRC were compared using Clinprot technology. Using enzyme-linked immunosorbent assays (ELISAs), 366 sera samples were additionally analyzed, and immunohistochemistry studies of 400 tissues were used to verify the expression of kininogen-1 and its value in the early detection of CRC.

Results

Predicting models were established among the three groups, and kininogen-1 was identified as a potential marker for CRC using Clinprot technology. ELISAs also detected significantly higher serum kininogen-1 levels in ACA and CRC patients compared to controls (P<0.05). Furthermore, the area under the receiver operating characteristic curve (AUC) for serum kininogen-1 in the diagnosis of ACA was 0.635 (P = 0.003), and for serum carcinoembryonic antigen (CEA) was 0.453 (P = 0.358). The sensitivity, specificity, and accuracy of serum kininogen-1 for diagnosing Duke’s stage A and B CRC was 70.13%, 65.88%, and 67.90%, respectively, whereas serum CEA was 38.96%, 85.88%, and 63.58%, respectively. Moreover, immunohistochemistry showed that expression of kininogen-1 was significantly higher in CRC and ACA tissues than in normal mucosa (48.39% vs. 15.58% vs. 0%, P<0.05).

Conclusions

These results suggest that Clinprot technology provides a useful tool for the diagnosis of CRC, and kininogen-1 is a potential serum biomarker for the early detection of advanced colorectal adenoma and CRC.     

Identification of Protein Biomarkers for Cervical Cancer Using Human Cervicovaginal Fluid

Objectives

Cervicovaginal fluid (CVF) can be considered as a potential source of biomarkers for diseases of the lower female reproductive tract. The fluid can easily be collected, thereby offering new opportunities such as the development of self tests. Our objective was to identify a CVF protein biomarker for cervical cancer or its precancerous state.

Methods

A differential proteomics study was set up using CVF samples from healthy and precancerous women. Label-free spectral counting was applied to quantify protein abundances.

Results

The proteome analysis revealed 16 candidate biomarkers of which alpha-actinin-4 (p = 0.001) and pyruvate kinase isozyme M1/M2 (p = 0.014) were most promising. Verification of alpha-actinin-4 by ELISA (n = 28) showed that this candidate biomarker discriminated between samples from healthy and both low-risk and high-risk HPV-infected women (p = 0.009). Additional analysis of longitudinal samples (n = 29) showed that alpha-actinin-4 levels correlated with virus persistence and clearing, with a discrimination of approximately 18 pg/ml.

Conclusions

Our results show that CVF is an excellent source of protein biomarkers for detection of lower female genital tract pathologies and that alpha-actinin-4 derived from CVF is a promising candidate biomarker for the precancerous state of cervical cancer. Further studies regarding sensitivity and specificity of this biomarker will demonstrate its utility for improving current screening programs and/or its use for a cervical cancer self-diagnosis test.     

Protein Microarrays for the Identification of Praja1 E3 Ubiquitin Ligase Substrates

Although they are the primary determinants of substrate specificity, few E3-substrate pairs have been positively identified, and few E3's profiled in a proteomic fashion. Praja1 is an E3 implicated in bone development and highly expressed in brain. Although it has been well studied relative to the majority of E3's, little is known concerning the repertoire of proteins it ubiquitylates. We sought to identify high confidence substrates for Praja1 from an unbiased proteomic profile of thousands of human proteins using protein microarrays. We first profiled Praja1 activity against a panel of E2's to identify its optimal partner in vitro. We then ubiquitylated multiple, identical protein arrays and detected putative substrates with reagents that vary in ubiquitin recognition according to the extent of chain formation. Gene ontology clustering identified putative substrates consistent with information previously known about Praja1 function, and provides clues into novel aspects of this enzyme's function.     

Blood-Based Protein Biomarker Panel for the Detection of Colorectal Cancer

Background

The majority of colorectal cancer (CRC) cases are preventable by early detection and removal of precancerous polyps. Even though CRC is the second most common internal cancer in Australia, only 30 per cent of the population considered to have risk factors participate in stool-based test screening programs. Evidence indicates a robust, blood-based, diagnostic assay would increase screening compliance. A number of potential diagnostic blood-based protein biomarkers for CRC have been reported, but all lack sensitivity or specificity for use as a stand-alone diagnostic. The aim of this study was to identify and validate a panel of protein-based biomarkers in independent cohorts that could be translated to a reliable, non-invasive blood-based screening test.

Principal Findings

In two independent cohorts (n = 145 and n = 197), we evaluated seven single biomarkers in serum of CRC patients and age/gender matched controls that showed a significant difference between controls and CRC, but individually lack the sensitivity for diagnostic application. Using logistic regression strategies, we identified a panel of three biomarkers that discriminated between controls and CRC with 73% sensitivity at 95% specificity, when applied to either of the two cohorts. This panel comprised of Insulin like growth factor binding protein 2 (IGFBP2), Dickkopf-3 (DKK3), and Pyruvate kinase M2(PKM2).

Conclusions

Due to the heterogeneous nature of CRC, a single biomarker is unlikely to have sufficient sensitivity or specificity for use as a stand-alone diagnostic screening test and a panel of markers may be more effective. We have identified a 3 biomarker panel that has higher sensitivity and specificity for early stage (Stage I and -II) disease than the faecal occult blood test, raising the possibility for its use as a non-invasive blood diagnostic or screening test.     

结直肠癌早期诊断的研究进展

结直肠癌(colorectal cancer,CRC)的早期诊断对减少肿瘤发病率和死亡率具有极其重要的意义。随着分子生物、内镜影像技术以及激光技术的发展,各种诊断方法不断改进,新诊断方法和技术不断涌现,对结直肠癌的早期诊断、定位和分期提高到了一个新的认知水平。本文简述了结直肠组织的层微结构和癌变进程,介绍了目前临床诊断的主要方法,展望了其发展方向。论文在重点评述非线性光谱技术,包括双光子激发荧光、二次谐波以及拉曼光谱在CRC诊断研究的基础上,提出联合多光子显微成像与拉曼光谱技术进一步开展结直肠癌早期无损诊断研究。     

Serum Vitamin D,Vitamin D Binding Protein,and Risk of Colorectal Cancer

Background

We previously reported a positive association between serum 25-hydroxyvitamin D (25(OH)D) and colorectal cancer risk. To further elucidate this association, we examined the molar ratio of 25(OH)D to vitamin D binding protein (DBP), the primary 25(OH)D transport protein, and whether DBP modified the association between 25(OH)D and colorectal cancer risk.

Methods

In a nested case-control study within the Alpha-Tocopherol, Beta-Carotene Cancer Prevention Study, controls were 1∶1 matched to 416 colorectal cancer cases based on age and date of blood collection. Logistic regression was used to estimate odds ratios (ORs) and 95% confidence intervals (CI) for quartiles of 25(OH)D, DBP, and the molar ratio of 25(OH)D:DBP, a proxy for free, unbound circulating 25(OH)D.

Results

Comparing highest to lowest quartiles, DBP was not associated with colorectal cancer risk (OR = 0.91; 95% CI: 0.58, 1.42, p for trend  = 0.58); however, a positive risk association was observed for the molar ratio of 25(OH)D:DBP (OR = 1.44; 95% CI: 0.92, 2.26, p for trend  = 0.04). In stratified analyses, the positive association between 25(OH)D and colorectal cancer was stronger among men with DBP levels above the median (OR = 1.89; 95% CI: 1.07, 3.36, p for trend  = 0.01) than below the median (OR = 1.20; 95% CI: 0.68, 2.12, p for trend  = 0.87), although the interaction was not statistically significant (p for interaction  = 0.24).

Conclusion

Circulating DBP may influence the association between 25(OH)D and colorectal cancer in male smokers, with the suggestion of a stronger positive association in men with higher DBP concentrations. This finding should be examined in other populations, especially those that include women and non-smokers.     

自体荧光技术在早期肠癌诊断中的应用

自体荧光技术以无损、实时、灵敏度高等优点已成为早期肠癌诊断应用的技术之一。本文总结了自体荧光光谱技术在早期肠癌诊断应用中的研究进展,重点阐述了荧光激发波长的选择,荧光光谱数据处理方法,以及正常和癌变肠道组织光谱差异的来源。在分析肠道组织中内源性荧光物质及其分布的基础上,回顾了自体荧光成像系统的临床应用进展。最后指出自体荧光光谱与成像技术在早期肠癌诊断中的应用和发展趋势。     

Identification of Novel Biomarkers for Metastatic Colorectal Cancer Using Angiogenesis-Antibody Array and Intracellular Signaling Array

Colorectal cancer (CRC) is one of the three leading causes for cancer mortality. CRC kills over 600,000 people annually worldwide. The most common cause of death from CRC is the metastasis to distant organs. However, biomarkers for CRC metastasis remain ill-defined. We compared primary and metastatic CRC cell lines for their angiogenesis-protein profiles and intracellular signaling profiles to identify novel biomarkers for CRC metastasis. To this end, we used primary and metastatic CRC cell lines as a model system and normal human colon cell line as a control. The angiogenesis profiles two isogenic CRC cell lines, SW480 and SW620, and HT-29 and T84 revealed that VEGF was upregulated in both SW620 and T84 whereas coagulation factor III, IGFBP-3, DPP IV, PDGF AA/AB, endothelin I and CXCL16 were downregulated specifically in metastatic cell lines. Furthermore, we found that TIMP-1, amphiregulin, endostatin, angiogenin were upregulated in SW620 whereas downregulated in T84. Angiogenin was downregulated in T84 and GM-CSF was also downregulated in SW620. To induce CRC cell metastasis, we treated cells with pro-inflammatory cytokine IL-6. Upon IL-6 treatment, epithelial-mesenchymal transition was induced in CRC cells. When DLD-1 and HT-29 cells were treated with IL-6; Akt, STAT3, AMPKα and Bad phosphorylation levels were increased. Interestingly, SW620 showed the same signal activation pattern with IL-6 treatment of HT-29 and DLD-1. Our data suggest that Akt, STAT3, AMPKα and Bad activation can be biomarkers for metastatic colorectal cancer. IL-6 treatment specifically reduced phosphorylation levels of EGFR, HER2 receptor, Insulin R and IGF-1R in receptor tyrosine kinase array study with HT-29. Taken together, we have identified novel biomarkers for metastatic CRC through the angiogenesis-antibody array and intracellular signaling array studies. Present study suggests that those novel biomarkers can be used as CRC prognosis biomarkers, and as potential targets for the metastatic CRC therapy.     

Colorectal Cancer Cell Surface Protein Profiling Using an Antibody Microarray and Fluorescence Multiplexing

The current prognosis and classification of CRC relies on staging systems that integrate histopathologic and clinical findings. However, in the majority of CRC cases, cell dysfunction is the result of numerous mutations that modify protein expression and post-translational modification¹.A number of cell surface antigens, including cluster of differentiation (CD) antigens, have been identified as potential prognostic or metastatic biomarkers in CRC. These antigens make ideal biomarkers as their expression often changes with tumour progression or interactions with other cell types, such as tumour-infiltrating lymphocytes (TILs) and tumour-associated macrophages (TAMs).The use of immunohistochemistry (IHC) for cancer sub-classification and prognostication is well established for some tumour types^2,3. However, no single ‘marker’ has shown prognostic significance greater than clinico-pathological staging or gained wide acceptance for use in routine pathology reporting of all CRC cases. A more recent approach to prognostic stratification of disease phenotypes relies on surface protein profiles using multiple ''markers''. While expression profiling of tumours using proteomic techniques such as iTRAQ is a powerful tool for the discovery of biomarkers4, it is not optimal for routine use in diagnostic laboratories and cannot distinguish different cell types in a mixed population. In addition, large amounts of tumour tissue are required for the profiling of purified plasma membrane glycoproteins by these methods. In this video we described a simple method for surface proteome profiling of viable cells from disaggregated CRC samples using a DotScan CRC antibody microarray. The 122-antibody microarray consists of a standard 82-antibody region recognizing a range of lineage-specific leukocyte markers, adhesion molecules, receptors and markers of inflammation and immune response⁵, together with a satellite region for detection of 40 potentially prognostic markers for CRC. Cells are captured only on antibodies for which they express the corresponding antigen. The cell density per dot, determined by optical scanning, reflects the proportion of cells expressing that antigen, the level of expression of the antigen and affinity of the antibody⁶. For CRC tissue or normal intestinal mucosa, optical scans reflect the immunophenotype of mixed populations of cells. Fluorescence multiplexing can then be used to profile selected sub-populations of cells of interest captured on the array. For example, Alexa 647-anti-epithelial cell adhesion molecule (EpCAM; CD326), is a pan-epithelial differentiation antigen that was used to detect CRC cells and also epithelial cells of normal intestinal mucosa, while Phycoerythrin-anti-CD3, was used to detect infiltrating T-cells⁷. The DotScan CRC microarray should be the prototype for a diagnostic alternative to the anatomically-based CRC staging system.     

Identification of Candidate Plasma Protein Biomarkers for Cervical Cancer Using the Multiplex Proximity Extension Assay

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Highlights

• •HPV is being introduced as the primary test in cervical cancer screening programs.
• •New biomarkers are needed for co-testing of women HPV positive in screening.
• •Analysis of plasma from women with invasive cervical cancer identified a 11-marker panel.
• •This signature shows high sensitivity and specificity to identify women with cancer.

     

Identification of Genes and Genomic Islands Correlated with High Pathogenicity in Streptococcus suis Using Whole Genome Tilling Microarrays

Streptococcus suis is an important zoonotic pathogen that can cause meningitis and sepsis in both pigs and humans. Infections in humans have been sporadic worldwide but two severe outbreaks occurred in China in recent years, while infections in pigs are a major problem in the swine industry. Some S. suis strains are more pathogenic than others with 2 sequence types (ST), ST1 and ST7, being well recognized as highly pathogenic. We analyzed 31 isolates from 23 serotypes and 25 STs by NimbleGen tiling microarray using the genome of a high pathogenicity (HP) ST1 strain, GZ1, as reference and a new algorithm to detect gene content difference. The number of genes absent in a strain ranged from 49 to 225 with a total of 632 genes absent in at least one strain, while 1346 genes were found to be invariably present in all strains as the core genome of S. suis, accounting for 68% of the GZ1 genome. The majority of genes are located in chromosomal blocks with two or more contiguous genes. Sixty two blocks are absent in two or more strains and defined as regions of difference (RDs), among which 26 are putative genomic islands (GIs). Clustering and statistical analyses revealed that 8 RDs including 6 putative GIs and 21 genes within these RDs are significantly associated with HP. Three RDs encode known virulence related factors including the extracellular factor, the capsular polysaccharide and a SrtF pilus. The strains were divided into 5 groups based on population genetic analysis of multilocus sequence typing data and the distribution of the RDs among the groups revealed gain and loss of RDs in different groups. Our study elucidated the gene content diversity of S. suis and identified genes that potentially promote HP.     

雄激素含量测定用蛋白微阵列的制备

利用分子生物学技术对鼠雄激素受体结合域(rARLBD)重组表达,结合新兴的蛋白质微阵列技术建立了一种快速无污染的检测方法,用于临床雄激素检测及新药发现。实验将编码ARLBD的cDNA片段(888bp)插入到含有多聚组氨酸标签的表达载体pET32a中构建了表达质粒pET32a/AR,并将其转化到大肠杆菌BL21中。经IPTG低温诱导,得到高效表达的可溶性ARLBD融合蛋白产物,并通过NiNTA凝胶亲和吸附纯化。将纯化得到的ARLBD使用芯片点样仪固定到硅烷化-多糖表面片基,制备得到ARLBD蛋白质微阵列。实验得到的特异性结合曲线表明在微阵列上的受体蛋白能够保持功能构像。通过Scatchard方程计算得到微阵列上ARLBD与荧光标记的睾酮结合的Kd值为5.32nmol/L。浓度依赖性标准曲线表明这一方法有较高的灵敏度,最低检测限达1pmol/L。应用这一方法对224例健康中国老年人血清雄激素水平进行了测定,研究证明了该方法的可靠性,并首次提供了一定样本量的我国老年人血清活性雄激素水平的参考值。这一技术的建立将为生物工程技术产品与临床检测和分子水平化合物筛选有效地结合提供一条新的途径。     

结直肠癌组织异常表达miRNA的鉴定

目的：筛选结直肠癌组织异常表达的miRNAs。方法：采用Agilem基因芯片（V12．0）分析结直肠癌组织及其配对正常粘膜组织间差异表达的miRNAs,MiRNAs错误发生率（FDR）〈0．05和微矩阵显著性分析（SAM）q值〈0．05为差异显著。结果：鉴定出结直肠癌中32个差异表达的miRNAs,显著上调和下调各16个。实时定量PCR（RT—qPCR）证实基因芯片中4个表达上调的miRNAs在结直肠癌组织中也显著上调。结论：MiRNA基因芯片鉴定出了结直肠癌组织一系列新的差异表达的miRNAs。     

散发性大肠癌血清多肽肿瘤标志物的高通量筛选

目的:以常规体检者和明确诊断的大肠癌患者为研究对象,对其血清进行多肽谱分析,统计分析获得大肠癌特异血清多肽峰,为大肠癌的分子诊断提供理论依据,提高大肠癌的早期诊断水平。方法:1)收集研究对象外周非抗凝血并记录其人口学特征,将非抗凝血进行离心分离血清并保存;2)用Dynabeads RPC18磁珠分离提取血清蛋白质,Bruker UltraFlex TOF/TOF采集信号并用分析软件Clinprot tools 2.2(Bruker)分析筛选出大肠癌血清显著差异峰;3)用SPSS13.0分析大肠癌患者和健康人多肽峰的差异,进行Logistic回归分析差异多肽对形成大肠癌的影响。结果:本次研究共获得111名健康人和94名大肠癌患者的血清多肽峰信息,其中109名健康人和91名大肠癌患者同时具有性别、年龄等人口学信息。筛选出差异多肽峰105个,其中76个多肽在大肠癌患者和健康人间的分布差异有统计学意义(P0.05)。运用Logistic回归分析,进入回归方程(P0.05)的有:年龄,质荷比(m/z)分别为1061.10、1213.09、1607.32、1867.02、1897.95、2011.67和5078.81的七种多肽。结论:液体蛋白芯片飞行时间质谱系统可高效、精确地筛查血清多肽。大肠癌患者与健康人的血清多肽存在差异,筛选得到的质荷比(m/z)分别为1061.10、1213.09、1607.32、1867.02、1897.95、2011.67和5078.81的七种多肽可能作为早期诊断大肠癌的潜在肿瘤标志物。     

Postoperative Serum Levels of sCD26 for Surveillance in Colorectal Cancer Patients

One of the main aims of the follow-up after curative resection of colorectal cancer is the early detection and treatment of tumor recurrence. We previously demonstrated decreased preoperative soluble CD26 (sCD26) levels in serum from colorectal cancer patients. We extended now the study to investigate if sCD26 levels in postoperative serum serve as marker of recurrence of the disease during surveillance. Soluble sCD26 was measured in pre- and postoperative serum samples of 43 patients with primary colorectal cancer. Carcinoembryonic antigen, carbohydrate antigen 19.9 and 72.4 levels were also measured during surveillance. The average follow-up period was 41.8±20.8 months. sCD26 levels during follow-up showed well-defined patterns in patients without disease (n = 28), and in patients with tumor persistence (n = 2), local recurrence (n = 3) or distant metastasis (n = 10). Disease-free patients showed stable levels between 460–850 ng/mL during follow-up, while high (over 850 ng/mL) and unstable sCD26 levels were found before recurrence was diagnosed. The mean maximum/minimum sCD26 ratios during surveillance were 1.52, 2.12 and 2.63 for patients with no recurrence, local recurrence and metastasis, respectively (p = 0.005). From the cut-off obtained from a receiver operator characteristics (ROC) curve built with the maximum/minimum sCD26 ratios and the upper and lower cut-offs of sCD26, we were able to discriminate patients with and without recurrent disease. We propose that the measurement of serum sCD26 during the follow-up of patients diagnosed of colorectal cancer could be valuable for the early detection of local and distant recurrence. A large, randomized, prospective trial should be performed to confirm our findings.