Cancer immunomics: using autoantibody signatures in the early detection of prostate cancer

Network Organization of Antibody Interactions in Sequence and Structure Space: the RADARS Model

Adaptive immunity in vertebrates is a complex self-organizing network of molecular interactions. While deep sequencing of the immune-receptor repertoire may reveal clonal relationships, functional interpretation of such data is hampered by the inherent limitations of converting sequence to structure to function. In this paper, a novel model of antibody interaction space and network, termed radial adjustment of system resolution, RAdial ADjustment of System Resolution (RADARS), is proposed. The model is based on the radial growth of interaction affinity of antibodies towards an infinity of directions in structure space, each direction corresponding to particular shapes of antigen epitopes. Levels of interaction affinity appear as free energy shells of the system, where hierarchical B-cell development and differentiation takes place. Equilibrium in this immunological thermodynamic system can be described by a power law distribution of antibody-free energies with an ideal network degree exponent of phi square, representing a scale-free fractal network of antibody interactions. Plasma cells are network hubs, memory B cells are nodes with intermediate degrees, and B1 cells function as nodes with minimal degree. Overall, the RADARS model implies that a finite number of antibody structures can interact with an infinite number of antigens by immunologically controlled adjustment of interaction energy distribution. Understanding quantitative network properties of the system should help the organization of sequence-derived predicted structural data.

High-throughput screening of T7 phage display and protein microarrays as a methodological approach for the identification of IgE-reactive components

Olive pollen and yellow mustard seeds are major allergenic sources with high clinical relevance. To aid with the identification of IgE-reactive components, the development of sensitive methodological approaches is required. Here, we have combined T7 phage display and protein microarrays for the identification of allergenic peptides and mimotopes from olive pollen and mustard seeds. The identification of these allergenic sequences involved the construction and biopanning of T7 phage display libraries of mustard seeds and olive pollen using sera from allergic patients to both biological sources together with the construction of phage microarrays printed with 1536 monoclonal phages from the third/four rounds of biopanning. The screening of the phage microarrays with individual sera from allergic patients enabled the identification of 10 and 9 IgE-reactive unique amino acid sequences from olive pollen and mustard seeds, respectively. Five immunoreactive amino acid sequences displayed on phages were selected for their expression as His6-GST tag fusion proteins and validation. After immunological characterization, we assessed the IgE-reactivity of the constructs. Our results show that protein microarrays printed with T7 phages displaying peptides from allergenic sources might be used to identify allergenic components -peptides, proteins or mimotopes- through their screening with specific IgE antibodies from allergic patients.

Ultrasensitive Antibody Detection by Agglutination-PCR (ADAP)

Antibodies are widely used biomarkers for the diagnosis of many diseases. Assays based on solid-phase immobilization of antigens comprise the majority of clinical platforms for antibody detection, but can be undermined by antigen denaturation and epitope masking. These technological hurdles are especially troublesome in detecting antibodies that bind nonlinear or conformational epitopes, such as anti-insulin antibodies in type 1 diabetes patients and anti-thyroglobulin antibodies associated with thyroid cancers. Radioimmunoassay remains the gold standard for these challenging antibody biomarkers, but the limited multiplexability and reliance on hazardous radioactive reagents have prevented their use outside specialized testing facilities. Here we present an ultrasensitive solution-phase method for detecting antibodies, termed antibody detection by agglutination-PCR (ADAP). Antibodies bind to and agglutinate synthetic antigen-DNA conjugates, enabling ligation of the DNA strands and subsequent quantification by qPCR. ADAP detects zepto- to attomoles of antibodies in 2 μL of sample with a dynamic range spanning 5-6 orders of magnitude. Using ADAP, we detected anti-thyroglobulin autoantibodies from human patient plasma with a 1000-fold increased sensitivity over an FDA-approved radioimmunoassay. Finally, we demonstrate the multiplexability of ADAP by simultaneously detecting multiple antibodies in one experiment. ADAP's combination of simplicity, sensitivity, broad dynamic range, multiplexability, and use of standard PCR protocols creates new opportunities for the discovery and detection of antibody biomarkers.

Serum Autoantibodies in Chronic Prostate Inflammation in Prostate Cancer Patients

BACKGROUND

Chronic inflammation is frequently observed on histological analysis of malignant and non-malignant prostate specimens. It is a suspected supporting factor for prostate diseases and their progression and a main cause of false positive PSA tests in cancer screening. We hypothesized that inflammation induces autoantibodies, which may be useful biomarkers. We aimed to identify and validate prostate inflammation associated serum autoantibodies in prostate cancer patients and evaluate the expression of corresponding autoantigens.

METHODS

Radical prostatectomy specimens of prostate cancer patients (N = 70) were classified into high and low inflammation groups according to the amount of tissue infiltrating lymphocytes. The corresponding pre-surgery blood serum samples were scrutinized for autoantibodies using a low-density protein array. Selected autoantigens were identified in prostate tissue and their expression pattern analyzed by immunohistochemistry and qPCR. The identified autoantibody profile was cross-checked in an independent sample set (N = 63) using the Luminex-bead protein array technology.

RESULTS

Protein array screening identified 165 autoantibodies differentially abundant in the serum of high compared to low inflammation patients. The expression pattern of three corresponding antigens were established in benign and cancer tissue by immunohistochemistry and qPCR: SPAST (Spastin), STX18 (Syntaxin 18) and SPOP (speckle-type POZ protein). Of these, SPAST was significantly increased in prostate tissue with high inflammation. All three autoantigens were differentially expressed in primary and/or castration resistant prostate tumors when analyzed in an inflammation-independent tissue microarray. Cross-validation of the inflammation autoantibody profile on an independent sample set using a Luminex-bead protein array, retrieved 51 of the significantly discriminating autoantibodies. Three autoantibodies were significantly upregulated in both screens, MUT, RAB11B and CSRP2 (p>0.05), two, SPOP and ZNF671, close to statistical significance (p = 0.051 and 0.076).

CONCLUSIONS

We provide evidence of an inflammation-specific autoantibody profile and confirm the expression of corresponding autoantigens in prostate tissue. This supports evaluation of autoantibodies as non-invasive markers for prostate inflammation.

Personalized medicine for cancer therapy: Lessons learned from tumor-associated antigens

Antibody signatures may become sophisticated screening tools for early diagnosis and the development of personalized anticancer treatments. We used biopanning to enrich the immune response of head and neck squamous cell carcinoma (HNSCC) patients. This method revealed a HNSCC-specific antibody signature and allowed for the discovery of a novel oncogene, L23.

Autoantibodies to tumor-associated antigens as biomarkers in human hepatocellular carcinoma (HCC)

Tumor-associated antigens (TAAs) recognized by cellular and/or humoral effectors of the immune system are attractive targets for diagnostic and therapeutic approaches to human cancer. Different approaches can be used to comprehensively characterize and validate the identified TAA/anti-TAA systems, which are potential biomarkers in cancer immunodiagnosis. Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide. The high fatality rate of HCC within one year after its detection might be partly attributed to a lack of diagnostic methods that enable the early detection. Our previous studies have shown that novel autoantibodies can appear which are not detected prior to pre-malignant conditions during transition from chronic liver disease to HCC. The hypothesis we advance is the transition to malignancy can be associated with autoantibody response to certain cellular proteins that might have some role in tumorigenesis. We propose that the information that the cancer patient’s immune system is conveying in the form of autoantibodies to tumor-associated antigens (TAAs) should be utilized to a greater extent in identifying early signs of tumorigenesis. In this review, we will focus on the important features of TAA and the possibility that autoantibodies to TAAs can be used as biomarkers in immunodiagnosis and prognosis of HCC.

A phase I dose escalation trial of vaccine replicon particles (VRP) expressing prostate-specific membrane antigen (PSMA) in subjects with prostate cancer

PSMA-VRP is a propagation defective, viral replicon vector system encoding PSMA under phase I evaluation for patients with castration resistant metastatic prostate cancer (CRPC). The product is derived from an attenuated strain of the alphavirus, Venezuelan Equine Encephalitis (VEE) virus, and incorporates multiple redundant safety features. In this first in human trial, two cohorts of 3 patients with CRPC metastatic to bone were treated with up to five doses of either 0.9×10(7)IU or 0.36×10(8)IU of PSMA-VRP at weeks 1, 4, 7, 10 and 18, followed by an expansion cohort of 6 patients treated with 0.36×10(8)IU of PSMA-VRP at weeks 1, 4, 7, 10 and 18. No toxicities were observed. In the first dose cohort, no PSMA specific cellular immune responses were seen but weak PSMA-specific signals were observed by ELISA. The remaining 9 patients, which included the higher cohort and the extension cohort, had no PSMA specific cellular responses. PSMA-VRP was well-tolerated at both doses. While there did not appear to be clinical benefit nor robust immune signals at the two doses studied, neutralizing antibodies were produced by both cohorts suggesting that dosing was suboptimal.

The current status of cancer biomarker research using tumour-associated antigens for minimal invasive and early cancer diagnostics

Tumour-associated antigens (TAA) can be detected prior to clinical diagnosis and thus would be ideal biomarkers for early detection of cancer using only a few microliters of a patient's serum. In this article we provide a summary of TAA screening and serum-profiling conducted for breast, prostate, lung and colon cancers. Different methodological approaches, including SEREX, SERPA, and phage display for TAA identification and TAA panels are summarised, and a revision of array based techniques is provided. The most promising studies performed on these cancers (performed with 80-400 serum samples, including controls) obtained sensitivities in a range of 44-95% and specificities of 80-100%. From the various studies reviewed, only one performed cross validation (AUC=0.71) in a prostate cancer study. Thus, albeit receiver operation characteristics are very promising, cross validation of most studies is still missing. Additionally, the concerted action of research groups for standardization of serum-TAA testing and cross validation is required. Along with today's technological options, the chances of establishing TAA biomarkers are now higher than ever before. This may also be true for confirmation and validation of already existing data, which is a prerequisite for implementation of TAA biomarkers into clinical diagnostics. This article is part of a Special Issue entitled: Integrated omics.

RNASET2--an autoantigen in anaplastic large cell lymphoma identified by protein array analysis

Characterising tumour-associated antigens (TAAs) not only represents an important approach to the identification of new diagnostic/prognostic markers, but can also provide information on disease processes and additional potential therapeutic targets. Preliminary screening of a protein macroarray, containing more than 12,000 different proteins, with sera from anaplastic lymphoma kinase (ALK)-negative and ALK-positive anaplastic large cell lymphoma (ALCL) patients identified ribonuclease and tumour suppressor protein Ribonuclease T2 (RNASET2), phosphatase lipid phosphate phosphatase-related protein type 3 (LPPR3) and apoptotic adaptor molecule Fas-associating protein (FADD) as ALK-negative ALCL-associated TAAs. Further validation of these observations was confirmed using the ALCL sera in reverse ELISAs. The circulating anti-RNASET2 autoantibodies present in ALCL patients' sera also recognised eukaryotically expressed RNASET2 protein. RNASET2 expression was then investigated in normal tissues and in lymphomas to explore its clinical potential. RNASET2 protein and mRNA levels showed highest expression in the spleen, leucocytes and pancreas. RNASET2 protein expression was not restricted to ALK-negative ALCL (81%), being expressed in ALK-positive ALCL (65%) as well as in a number of other lymphomas. The immunological recognition of RNASET2, its expression in ALCL and other lymphomas together with its known tumourigenic properties suggest that further studies on this autoantigen are warranted.

Yeast surface display-based microfluidic immunoassay

In this paper, we present a new microfluidic immunoassay platform, which is based on the synergistic combination of the yeast surface display (YSD) technique and the microfluidic technology. Utilizing the YSD technique, antigens specific to the target antibody are displayed on the surface of engineered yeast cells with intracellular fluorescent proteins. The displayed antigens are then used for the detection of the target antibody, with the yeast cells as fluorescent labels. Multiplex immunoassay can be readily realized by using yeast cells expressing different intracellular fluorescent proteins to display different antigens. The implementation of this YSD-based immunoassay on the microfluidic platform eliminates the need for the bulky, complex and expensive flow cytometer. To improve the detection sensitivity and to eliminate the need for pumping, a functionalized micro pillar array (MPA) is incorporated in the microfluidic chip, resulting in a detection limit of 5 ng/mL (or 1 ng in terms of amount) and enhanced compatibility with practical applications such as clinical biopsy. This new platform has a high potential to be integrated into microfluidic detection systems to enable portable diagnostics in the future.

Serum-autoantibodies for discovery of prostate cancer specific biomarkers

BACKGROUND

The currently used prostate cancer serum marker has a low cancer specificity and improved diagnostics are needed. Here we evaluated whether autoantibodies are present in sera of prostate cancer patients and whether they are useful diagnostic markers for prostate cancer.

METHODS

Sera from 20 prostate cancer patients and 20 healthy controls were incubated on expression clone arrays containing more than 37,000 recombinant human proteins. Functional annotation clustering of the identified autoantigens was performed using the DAVID database. Autoantigens identified in the prostate cancer group were validated on microarrays using sera of 40 prostate cancer patients, 40 patients with elevated PSA levels but prostate cancer negative biopsies (benign disease), and 40 healthy controls.

RESULTS

We detected autoantibodies against 408 different antigens in sera of prostate cancer patients. One hundred seventy-four of these were exclusively detected in the cancer group compared to the healthy control group. Functional annotation clustering revealed an enrichment of RNA-associated, cytoskeleton, and nuclear proteins. The autoantibody panel was validated in serum samples of independent prostate cancer patients. Autoantibody profiles discriminated between prostate cancer patients and benign disease patients with an ROC curve AUC of 0.71. TTLL12, a protein recently described to be over-expressed in prostate cancer, was the highest ranked discrimination autoantigen.

CONCLUSION

A variety of autoantibodies were identified in sera of prostate cancer patients and provide a first step towards autoantibody diagnostics. Serum autoantibodies reflect the disease and represent valuable tools not only for prostate cancer, but also for other diseases affecting the immune response.

Autoantibodies against p53 are associated with chromosome 17p deletions in chronic lymphocytic leukemia

Autoantibodies against p53 have been observed in many cancers, often linked with abnormalities in the TP53 gene. Since p53 mutations and deletions at chromosome 17p are known to occur in CLL, we measured anti-p53 autoantibodies by ELISA in plasma samples from patients with normal cytogenetics as well as those with 13q, 11q, and 17p deletions as well as trisomy 12. Anti-p53 autoantibodies were detected in over half of the patients with a 17p deletion but in very few of the others. There was no correlation between the levels of anti-p53 antibodies and the percentage of cells with 17p abnormalities. The levels of the anti-p53 autoantibodies remained stable for most patients with serial samples. Increased levels of antibodies that bound to two peptide fragments of p53 were also seen in patients with 17p deletions. At least on case with high levels of anti-p53 autoantibodies had a heterozygotic mutation known to result in a dominant negative phenotype, suggesting that aberrant expression of p53 may contribute to the development of autoantibodies and suggests that these autoantibodies may reflect biological features relevant to prognosis.

Antibody responses to prostate-associated antigens in patients with prostatitis and prostate cancer

BACKGROUND

An important focus of tumor immunotherapy has been the identification of appropriate antigenic targets. Serum-based screening approaches have led to the discovery of hundreds of tumor-associated antigens recognized by IgG. Our efforts to identify immunologically recognized proteins in prostate cancer have yielded a multitude of antigens; however, prioritizing these antigens as targets for evaluation in immunotherapies has been challenging. In this report, we set out to determine whether the evaluation of multiple antigenic targets would allow the identification of a subset of antigens that are common immunologic targets in patients with prostate cancer.

METHODS

Using a phage immunoblot approach, we evaluated IgG responses in patients with prostate cancer (n = 126), patients with chronic prostatitis (n = 45), and men without prostate disease (n = 53).

RESULTS

We found that patients with prostate cancer or prostatitis have IgG specific for multiple common antigens. A subset of 23 proteins was identified to which IgG were detected in 38% of patients with prostate cancer and 33% patients with prostatitis versus 6% of controls (P < 0.001 and P = 0.003, respectively). Responses to multiple members were not higher in patients with advanced disease, suggesting antibody immune responses occur early in the natural history of cancer progression.

CONCLUSIONS

These findings suggest an association between inflammatory conditions of the prostate and prostate cancer, and suggest that IgG responses to a panel of commonly recognized prostate antigens could be potentially used in the identification of patients at risk for prostate cancer or as a tool to identify immune responses elicited to prostate tissue.

Identification of cancer autoantigens in serum: toward diagnostic/prognostic testing?

The development of noninvasive screening tests would represent a major advance in the fight against cancer, as pre-clinical or early diagnosis could be considered the best weapons to reduce cancer mortality. The use of autoantibodies against cancer autoantigens is a promising alternative to fulfill this goal. Recent progress in protein microarray formats and other proteomic strategies has brought extraordinary opportunities to advance the discovery of new cancer autoantigens. These new approaches have allowed identification of autoantibodies with a higher prevalence, simplifying the development of predictor panels with wider coverage. Still, some issues have to be resolved before clinical application of these results. First, technical limitations in the quality and reproducibility of the microarrays and the statistical tools for data analysis have to be resolved. Second, thorough validation of the candidate biomarkers has to be carried out to include not just one particular cancer type but different cancers and other benign, inflammatory pathologies, which may give rise to cross-reactions and loss of the specificity and sensitivity of the predictive assay. The extraordinary sensitivity of the immune system to detect minor alterations in self-proteins might be used to highlight changes in the cancer protein sequence and structure that can be used for personalized therapy, including immunotherapeutic vaccines. The increasing detection of kinase proteins as autoantibody targets points to new molecules with potential therapeutic impact.

Identification of cancer autoantigens in serum: toward diagnostic/prognostic testing?

The development of noninvasive screening tests would represent a major advance in the fight against cancer, as pre-clinical or early diagnosis could be considered the best weapons to reduce cancer mortality. The use of autoantibodies against cancer autoantigens is a promising alternative to fulfill this goal. Recent progress in protein microarray formats and other proteomic strategies has brought extraordinary opportunities to advance the discovery of new cancer autoantigens. These new approaches have allowed identification of autoantibodies with a higher prevalence, simplifying the development of predictor panels with wider coverage. Still, some issues have to be resolved before clinical application of these results. First, technical limitations in the quality and reproducibility of the microarrays and the statistical tools for data analysis have to be resolved. Second, thorough validation of the candidate biomarkers has to be carried out to include not just one particular cancer type but different cancers and other benign, inflammatory pathologies, which may give rise to cross-reactions and loss of the specificity and sensitivity of the predictive assay. The extraordinary sensitivity of the immune system to detect minor alterations in self-proteins might be used to highlight changes in the cancer protein sequence and structure that can be used for personalized therapy, including immunotherapeutic vaccines. The increasing detection of kinase proteins as autoantibody targets points to new molecules with potential therapeutic impact.

RHAMM (CD168) is overexpressed at the protein level and may constitute an immunogenic antigen in advanced prostate cancer disease

Localized prostate cancer (CaP) can be cured using several strategies. However, the need to identify active substances in advanced tumor stages is tremendous, as the outcome in such cases is still disappointing. One approach is to deliver human tumor antigen-targeted therapy, which is recognized by T cells or antibodies. We used data mining of the Cancer Immunome Database (CID), which comprises potential immunologic targets identified by serological screening of expression libraries. Candidate antigens were screened by DNA microarrays. Genes were then validated at the protein level by tissue microarrays, representing various stages of CaP disease. Of 43 targets identified by CID, 10 showed an overexpression on the complementary DNA array in CaP metastases. The RHAMM (CD168) gene, earlier identified by our group as an immunogenic antigen in acute and chronic leukemia, also showed highly significant overexpression in CaP metastases compared with localized disease and benign prostatic hyperplasia. At the protein level, RHAMM was highest in metastatic tissue samples and significantly higher in neoplastic localized disease compared with benign tissue. High RHAMM expression was associated with clinical parameters known to be linked to better clinical outcome. Patients with high RHAMM expression in the primaries had a significantly lower risk of biochemical failure. The number of viable cells in cell cultures was reduced in blocking experiments using hormone-sensitive and hormone-insensitive metastatic CaP cell lines. Acknowledging the proven immunogenic effects of RHAMM in leukemia, this antigen is intriguing as a therapeutic target in far-advanced CaP.

Molecular biomarkers in prostate cancer

BACKGROUND

After more than two decades of clinical use, serum prostate-specific antigen (PSA) has increased the early diagnosis of prostate cancer, detecting the disease even when small volumes are present. Although stage migration of prostate cancer has occurred, PSA has well-known limitations, despite attempts at refinement and modification, such as the use of PSA velocity, which have been used to improve it. New biomarkers for prostate cancer have been discovered, with promising early results.

OBJECTIVE/METHODS

This article reviews the ubiquitous current literature on biomarkers in prostate cancer. A search using MEDLINE and EMBASE databases was performed and those articles reporting biomarkers in prostate cancer with clinically significant findings in terms of detection were analyzed. Immunohistochemical markers were not considered for this review.

RESULTS/CONCLUSION

Despite many markers being promising, no single marker has satisfied the criteria as a perfect candidate. Limited clinical use of IL-6, TGF-β1 and PCA3 has commenced, and further widespread availability of these tests is expected in the coming years. The future lies in artificial neural networks and panels of markers instead of individual assays. Although PSA has some well-known limitations, it is at present the best marker available for prostate cancer when used in conjunction with nomograms or risk calculators.

Proteomic profiling of serologic response to Candida albicans during host-commensal and host-pathogen interactions

Candida albicans is a commensal inhabitant of the normal human microflora that can become pathogenic and invade almost all body sites and organs in response to both host-mediated and fungus-mediated mechanisms. Serologic responses to C. albicans that underlie its dichotomist relationship with the host (host-commensal and host-pathogen interactions) display a high degree of heterogeneity, resulting in distinct serum anti-Candida antibody signatures (molecular fingerprints of anti-Candida antibodies in serum) that can be used to discriminate commensal colonization from invasive disease. We describe the typical proteomic strategy to globally and integratively profile these host antibody responses and determine serum antibody signatures. This approach is based on the combination of classic immunoproteomics or serologic proteome analysis (two-dimensional electrophoresis followed by quantitative Western blotting and mass spectrometry) with data mining procedures. This global proteomic stratagem is a useful tool not only for obtaining an overview of different anti-Candida antibodies that are being elicited during the host-fungus interaction and, consequently, of the complex C. albicans immunome (the subset of the C. albicans proteome targeted by the immune system), but also for evaluating how this pathogen organism interacts with its host to trigger infection. In contrast with genomics and transcriptomics, this proteomic technology has the potential to detect antigenicity associated with posttranslational modification, subcellular localization, and other functional aspects that can be relevant in the host immune response. Furthermore, this strategy to define molecular fingerprints of serum anti-Candida antibodies may hopefully bring to light potential candidates for diagnosis, prognosis, risk stratification, clinical follow-up, therapeutic monitoring, and/or immunotherapy of candidiasis, especially of its life-threatening systemic forms.

Monitoring B cell response to immunoselected phage-displayed peptides by microarrays

Successful adaptation of microarray technology for high-throughput screening of proteins requires a large number of purified recombinant proteins, e.g., antibodies for use as capture molecules. Phage surface display technology has been used for the surface expression of proteins, peptides or cDNA repertoires expressed by tumor cells. It does not require protein purification, as recombinant phages can be spotted on glass slides and used in a high-throughput screening format. Biopanning of phage libraries on patient serum antibodies is expected to enrich for antibody-binding phages for the fabrication of diagnostic and/or prognostic B-cell epitope microarrays. In contrast to other immunological techniques, microarrays can measure the antibody levels against different epitopes in a single test. This chapter highlights the recent advances in phage-based microarray technology to profile humoral immune responses in cancer patients.

Identifying novel autoantibody signatures in ovarian cancer using high-density protein microarrays

OBJECTIVES

To identify autoantibody signatures in ovarian cancer using protein microarray technology.

DESIGN AND METHODS

Protein microarrays were screened using non-malignant peritoneal fluid (n=30) and ascites fluid pooled from ovarian cancer patients (n=30).

RESULTS

Fifteen potential tumour-associated antigens were discovered. AASDHPPT showed the strongest signal-to-noise ratio.

CONCLUSIONS

Protein microarrays are suitable for autoantibody discovery in ovarian cancer but the signatures are of low frequency.

Profiling antibody responses by multiparametric analysis of primary B cells

Determining the efficacy of a vaccine generally relies on measuring neutralizing antibodies in sera. This measure cannot elucidate the mechanisms responsible for the development of immunological memory at the cellular level, however. Quantitative profiles that detail the cellular origin, extent, and diversity of the humoral (antibody-based) immune response would improve both the assessment and development of vaccines. Here, we describe a novel approach to collect multiparametric datasets that describe the specificity, isotype, and apparent affinity of the antibodies secreted from large numbers of individual primary B cells (approximately 10(3)-10(4)). The antibody/antigen binding curves obtained by this approach can be used to classify closely related populations of cells using algorithms for data clustering, and the relationships among populations can be visualized graphically using affinity heatmaps. The technique described was used to evaluate the diversity of antigen-specific antibody-secreting cells generated during an in vivo humoral response to a series of immunizations designed to mimic a multipart vaccination. Profiles correlating primary antibody-producing cells with the molecular characteristics of their secreted antibodies should facilitate both the evaluation of candidate vaccines and, broadly, studies on the repertoires of antibodies generated in response to infectious or autoimmune diseases.

Profiling tumor-associated autoantibodies for the detection of colon cancer

PURPOSE

The purpose of the present study was to screen the autoantibody signature of colon cancers to develop serum markers for colon cancer detection.

EXPERIMENTAL DESIGN

A phage cDNA expression library of colon cancer was built. The library was sequentially screened by a pool of 10 colon cancer sera, goat antihuman IgG, and a pool of two healthy sera to identify phage-expressed antigens recognized by tumor-associated antibodies. The clones picked out by these screening were subjected to a training set with 24 colon cancer sera and 24 healthy sera. The antigen combination, which got the most satisfactory classification, was tested by an independent set of 24 colon cancer sera with equal number of sera from normal donors. The carcinoembryonic antigen (CEA) level of these sera was detected for the additional classification analysis with or without the antigen combination.

RESULTS

A cDNA expression library consisting of 2 x 10(6) primary clones was prepared. After three turns of screening, 24 antigens recognized by tumor-associated antibodies were picked out for serum marker identification. The training set showed that a six-marker combination got the most satisfactory classification in a logistic regression model; leave-one-out validation achieved 91.7% sensitivity and 91.7% specificity. In a testing set with this marker panel, we correctly predicted 85% of the samples. Although according to CEA level alone, we correctly predicted 75% of the samples with 42% of cancer patients misclassified. When CEA was combined with the six markers, the sensitivity and specificity increased to 91.7% and 95.8%, respectively. The six antigen sequences in the phage display system are relatively short peptides. Only two of them showed homology to known protein sequences.

CONCLUSIONS

Autoantibodies against phage-expressed antigens derived from colon cancer tissues could be used as serum markers for the detection of colon cancer.

Functions of normal and malignant prostatic stem/progenitor cells in tissue regeneration and cancer progression and novel targeting therapies

This review summarizes the recent advancements that have improved our understanding of the functions of prostatic stem/progenitor cells in maintaining homeostasis of the prostate gland. We also describe the oncogenic events that may contribute to their malignant transformation into prostatic cancer stem/progenitor cells during cancer initiation and progression to metastatic disease stages. The molecular mechanisms that may contribute to the intrinsic or the acquisition of a resistant phenotype by the prostatic cancer stem/progenitor cells and their differentiated progenies with a luminal phenotype to the current therapies and disease relapse are also reviewed. The emphasis is on the critical functions of distinct tumorigenic signaling cascades induced through the epidermal growth factor system, hedgehog, Wnt/beta-catenin, and/or stromal cell-derived factor-1/CXC chemokine receptor-4 pathways as well as the deregulated apoptotic signaling elements and ATP-binding cassette multidrug transporter. Of particular therapeutic interest, we also discuss the potential beneficial effects associated with the targeting of these signaling elements to overcome the resistance to current treatments and prostate cancer recurrence. The combined targeted strategies toward distinct oncogenic signaling cascades in prostatic cancer stem/progenitor cells and their progenies as well as their local microenvironment, which could improve the efficacy of current clinical chemotherapeutic treatments against incurable, androgen-independent, and metastatic prostate cancers, are also described.

Clinical proteomics: discovery of cancer biomarkers using mass spectrometry and bioinformatics approaches--a prostate cancer perspective

Prostate cancer (PCa) is an intractable disease, where diagnosis and clinical prediction of the disease course and response to treatment is compromised by the lack of objective and robust biomarker assays. In late stage metastatic disease, treatment options are limited, although it is recognized that some patients may benefit from immunotherapy and in particular vaccine therapy. However, research into biomarkers that correlate with the clinical outcome of immunotherapy has lagged behind vaccine development. Thus, proteomic tools are increasingly being utilized for the discovery of biomarkers which will allow us to make clinical decisions about patient treatment at an earlier stage and should aid in shortening the development time for vaccines. In this review we will summarize the various proteomic platforms used to investigate new biomarkers in PCa for better patient diagnosis, prognosis, patient stratification, treatment monitoring and clinical surrogate endpoints. We will discuss method limitations and highlight the key areas of research required for understanding the etiology of PCa.

MAD-CT-2 identified as a novel melanoma cancer-testis antigen using phage immunoblot analysis

One focus in the field of tumor immunology is the identification of cancer-specific antigens that might be exploited as therapeutic targets or as immunologic diagnostic markers. Cancer-testis antigens (CTAs) are of particular interest as potential target antigens given that their expression is typically restricted to germ cells among normal tissues, but aberrantly expressed in multiple tumor types. In the current report, we sought to evaluate serum antibody immune responses to a defined panel of CTA from multiple antigen families to identify potential tumor-specific antigens that could potentially serve as candidate target antigens for immunotherapy or diagnostic purposes. This was conducted by screening sera from male patients with metastatic melanoma (n=44) and volunteer blood donors (n=50) against a panel of lambda phage-encoded CTA. We found that IgG antibody responses occurred in 39% of patients with melanoma to at least one of these antigens compared with 4% of controls (P<0.001). We found antibody responses to one antigen, MAD-CT-2, occurred in 27% of patients compared with 0/50 controls (P<0.0001). These findings, along with the demonstration that MAD-CT-2 is expressed in melanoma cell lines, identified MAD-CT-2 as a novel melanoma CTA.

[Protein arrays and perspectives of medical applications]

Protein microarrays make it possible to detect molecular interactions with various partners (proteins, peptides, nucleic acids, sugars, etc.). Their advantages are crucial for high-throughput analysis of proteomes of different organisms. Moreover, the recent data reveal the performance of microarrays over current immunological methods. Therefore, the antigen and antibody microarrays become indispensable for medical applications, in particular, for diagnosis and prognosis of microbial infections, autoimmune and allergic diseases. The further technological progress might provide the extension of the miniaturized assays for multiparametric monitoring of human pathologies in practical medicine.

Cyclin B1 is commonly expressed in the cytoplasm of primary human acute myelogenous leukemia cells and serves as a leukemia-associated antigen associated with autoantibody response in a subset of patients

OBJECTIVES

Aberrant expression of cyclin B1, a cell cycle regulator, is related to prognosis in various human malignancies. Additionally, cytoplasmic expression of cyclin B1 in epithelial malignancies is associated with a specific T-cell response and presumably also a humoral immune response. We therefore investigated (i) whether a similar expression pattern could be detected in native human acute myelogenous leukemia (AML) cells and (ii) whether cyclin B1 specific antibodies could be detected in AML.

METHODS

AML cell expression of cyclin B1 was analyzed by flow cytometry and confocal microscopy. Humoral immune response in AML patient sera against cyclin B1 was analyzed by ELISA.

RESULTS

AML cell expression of cyclin B1 was detected for all 42 patients; but the percentage of cyclin B1 positive cells showed a wide variation between patients. Confocal microscopy demonstrated that 32/42 (76%) patient samples showed abnormal cytoplasmic expression. Furthermore, the cytoplasmic expression was maintained after 14 d of in vitro culture and differentiation of the AML cells towards a dendritic cell phenotype. Cyclin B1 specific serum antibodies could be detected for seven of 65 patients with untreated AML.

CONCLUSIONS

Our studies demonstrate that primary human AML cells show aberrant cytoplasmic expression of cyclin B1 for a majority of patients and a specific humoral immune response was also detected for a subset of patients with untreated leukemia.

Targeting serum antibody for cancer diagnosis: a focus on colorectal cancer

The ability of the immune system to magnify the appearance of disease by generating relatively large amounts of antibody in response to small amounts of disease makes it a natural biosensor, and serum antibodies have emerged as promising biomarkers for the detection of cancer. This review summarizes recent progress in targeting serum antibodies for cancer diagnosis, with a particular focus on colorectal cancer (CRC). Several serum antibodies have been detected at increased levels in CRC patients, including p53, carcinoembryonic antigen, Ras, topoisomerase II-alpha, histone deacetylase 3 and 5, ubiquitin C-terminal hydrolase L3, tropomyosin and cyclin B1. As each antibody is only present in a limited proportion of patients (usually < 40%), a combination of serum antibodies that defines the 'immunological signature' of cancer needs to be developed. High-throughput methods to identify new serum antibodies for cancer diagnosis are also reviewed.

Cancer immunomics using autoantibody signatures for biomarker discovery

The increased incidence of autoantibodies in malignancies has been described since the 1970s. Thus the ability to determine molecular fingerprinting of autoantibodies (antibody signatures) may provide useful clinical diagnostic and prognostic information. This review describes the use of several proteomics approaches for the identification of antigens recognized by these autoantibodies. Serological proteome analysis combines separation of tumor cell proteins on two-dimensional gel electrophoresis gels, Western blotting with sera of patients and healthy subjects, and identification of the detected antigens by MS. Alternatively multiple affinity protein profiling combines isolation of the antigens recognized by patient antibodies by two-dimensional immunoaffinity chromatography and identification by MS/MS. The use and limitations of reverse phase protein microarrays for testing patient serum containing autoantibodies are also considered. Lastly the most important difficulty of any proteomically identified autoantibody signature is validation in patient cohorts or clinical samples.

High throughput proteomic strategies for identifying tumour-associated antigens

Tumours elicit an immune response in the host organism and this area has been studied for decades. Initially, tumour-associated antigens were studied by examining a few proteins at a time using techniques such as 1-D SDS-PAGE and sandwich ELISAs. Now, however, with the development of high-throughput strategies, multiple potential antigens in a single experiment could be uncovered. The prevailing view is that these antigens can be used as biosensors for cancers. In addition, some of these antigens may indeed be used as targets for immunotherapy. SEREX, SERPA, and protein microarray technology have been the three dominant strategies employed to identify tumour-associated antigens. In this mini-review, we aim to describe these three techniques and provide their advantages and disadvantages. In addition, we aim to address some of the challenges of cancer immunomics.

The ageing male reproductive tract

Ageing of the male reproductive system is characterized by changes in the endocrine system, hypogonadism, erectile dysfunction and proliferative disorders of the prostate gland. Stochastic damage accumulating within ageing leads to progressive dysregulation at each level of the hypothalamic-pituitary-gonadal (HPG) axis and in local auto/paracrine interactions, thereby inducing morphological changes in reproductive target organs, such as the prostate, testis and penis. Despite age-related changes in the HPG axis, endocrine functions are generally sufficient to maintain fertility in elderly men. Ageing of the male reproductive system can give rise to clinically relevant manifestations, such as benign prostatic hyperplasia (BPH), prostate cancer (PCa) and erectile dysfunction (ED). In this review, we discuss morphological/histological changes occurring in these organs and current views and concepts of the underlying pathology. Moreover, we emphasize the molecular/cellular pathways leading to reduced testicular/penile function and proliferative disorders of the prostate gland.