High-sensitivity array analysis of gene expression for the early detection of disseminated breast tumor cells in peripheral blood

Assessment and prediction of glioblastoma therapy response: challenges and opportunities

Glioblastoma is the most aggressive type of primary adult brain tumour. The median survival of patients with glioblastoma remains approximately 15 months, and the 5-year survival rate is <10%. Current treatment options are limited, and the standard of care has remained relatively constant since 2011. Over the last decade, a range of different treatment regimens have been investigated with very limited success. Tumour recurrence is almost inevitable with the current treatment strategies, as glioblastoma tumours are highly heterogeneous and invasive. Additionally, another challenging issue facing patients with glioblastoma is how to distinguish between tumour progression and treatment effects, especially when relying on routine diagnostic imaging techniques in the clinic. The specificity of routine imaging for identifying tumour progression early or in a timely manner is poor due to the appearance similarity of post-treatment effects. Here, we concisely describe the current status and challenges in the assessment and early prediction of therapy response and the early detection of tumour progression or recurrence. We also summarize and discuss studies of advanced approaches such as quantitative imaging, liquid biomarker discovery and machine intelligence that hold exceptional potential to aid in the therapy monitoring of this malignancy and early prediction of therapy response, which may decisively transform the conventional detection methods in the era of precision medicine.

Single Particle Automated Raman Trapping Analysis of Breast Cancer Cell-Derived Extracellular Vesicles as Cancer Biomarkers

Extracellular vesicles (EVs) secreted by cancer cells provide an important insight into cancer biology and could be leveraged to enhance diagnostics and disease monitoring. This paper details a high-throughput label-free extracellular vesicle analysis approach to study fundamental EV biology, toward diagnosis and monitoring of cancer in a minimally invasive manner and with the elimination of interpreter bias. We present the next generation of our single particle automated Raman trapping analysis─SPARTA─system through the development of a dedicated standalone device optimized for single particle analysis of EVs. Our visualization approach, dubbed dimensional reduction analysis (DRA), presents a convenient and comprehensive method of comparing multiple EV spectra. We demonstrate that the dedicated SPARTA system can differentiate between cancer and noncancer EVs with a high degree of sensitivity and specificity (&gt;95% for both). We further show that the predictive ability of our approach is consistent across multiple EV isolations from the same cell types. Detailed modeling reveals accurate classification between EVs derived from various closely related breast cancer subtypes, further supporting the utility of our SPARTA-based approach for detailed EV profiling.

Inflammatory gene mRNA expression in human peripheral blood and its association with colorectal cancer

Objective

The present study planned to investigate the changes in the mRNA expression of inflammatory genes and their association with colorectal cancer (CRC). Our findings could be useful for noninvasive early screening of CRC patients.

Patients and methods

Venous blood of 20 CRC cases and 15 healthy controls was collected. The mRNA expression of COX-2, TNF-α, NF-κB and IL-6 genes was carried out by using real-time polymerase chain reaction. Relative quantification was done to find out the fold change of these genes.

Results

The mean age of cases and controls was 55 and 50 years, respectively. The ΔCt of COX-2, TNF-α, NF-κB and IL-6 genes was significantly (p < 0.05) lower in cases as compared to controls. Subsequently, the mRNA expression of these genes was, respectively, 3.56-, 3.4-, 1.71- and 3.86-fold higher in CRC cases as compared to controls. Positive correlation of ΔCt of COX-2 was found with ΔCt of TNF-α (r = 0.461, p = 0.041) and NF-κB (r = 0.536, p = 0.015) in CRC cases. The mRNA expression of COX-2 was significantly lower in T2 stage, while mRNA expression of NF-κB was significantly lower in both T2 and T3 stages of CRC as compared to T4 stage.

Conclusion

The increased mRNA expression of COX-2 along with the high mRNA expression of TNF-α, NF-κB and IL-6 genes may be associative risk factors for CRC. COX-2 and NF-κB genes were more expressed in advanced stages of CRC indicating their role in tumor progression. Our findings support the possible role of blood biomarker in the screening of CRC patients in the early stages.

Mammalian target of rapamycin complex 2 signaling in obese women changes after bariatric surgery

OBJECTIVES

After bariatric surgery, modifications to signaling pathway networks including those of the metabolic regulator called mammalian or mechanistic target of rapamycin (mTOR) may lead to molecular alterations related to energy source availability, systemic nutrients, and catabolic and anabolic cellular processes. This study aimed to identify gene expression changes with regard to the mTOR complex 2 subunit signaling pathway in obese patients before and after bariatric surgery.

METHODS

The experimental group included 13 obese women who were examined before (preoperative) and 6 mo after (postoperative) Roux-en-Y gastric bypass (RYGB) surgery. The control group included nine apparently eutrophic women matched by age and without any other metabolic diseases (i.e., no diabetes and no liver or kidney diseases). Peripheral blood mononuclear cell samples were collected for RNA extraction and subsequent microarray analysis.

RESULTS

After this methodological procedure, we identified 47 000 differentially expressed genes. A subsequent bioinformatic analysis showed that three diferentially expressed genes (rapamycin-insensitive companion of mTOR [RICTOR], phosphoinositide-3-kinase regulatory subunit 1 [PIK3 R1], and hypoxia inducible factor 1 alpha subunit 1A [HIF1 A]) participated in the mTOR signaling pathway. Real-time quantitative polymerase chain reaction revealed that RICTOR, PIK3 R1, and HIF1 A were upregulated 6 mo after RYGB surgery (P <0.05). In addition, patients in the experimental group lost weight significantly and presented significant improvement in biochemical/metabolic variables.

CONCLUSIONS

The weight loss that was induced by RYGB surgery alters the mTOR signaling pathway and specifically the mTOR complex 2 subunit. The increased expression of genes that act in this pathway such as RICTOR, PIK3 R1, and HIF1 A reflects the induced weight loss and improved metabolic indicators (e.g., insulin resistance and lipolysis) that are evidenced in this study.

Bioactive Nutrients and Nutrigenomics in Age-Related Diseases

The increased life expectancy and the expansion of the elderly population are stimulating research into aging. Aging may be viewed as a multifactorial process that results from the interaction of genetic and environmental factors, which include lifestyle. Human molecular processes are influenced by physiological pathways as well as exogenous factors, which include the diet. Dietary components have substantive effects on metabolic health; for instance, bioactive molecules capable of selectively modulating specific metabolic pathways affect the development/progression of cardiovascular and neoplastic disease. As bioactive nutrients are increasingly identified, their clinical and molecular chemopreventive effects are being characterized and systematic analyses encompassing the "omics" technologies (transcriptomics, proteomics and metabolomics) are being conducted to explore their action. The evolving field of molecular pathological epidemiology has unique strength to investigate the effects of dietary and lifestyle exposure on clinical outcomes. The mounting body of knowledge regarding diet-related health status and disease risk is expected to lead in the near future to the development of improved diagnostic procedures and therapeutic strategies targeting processes relevant to nutrition. The state of the art of aging and nutrigenomics research and the molecular mechanisms underlying the beneficial effects of bioactive nutrients on the main aging-related disorders are reviewed herein.

Viral Inhibition of the IFN-Induced JAK/STAT Signalling Pathway: Development of Live Attenuated Vaccines by Mutation of Viral-Encoded IFN-Antagonists

The interferon (IFN) induced anti-viral response is amongst the earliest and most potent of the innate responses to fight viral infection. The induction of the Janus kinase/signal transducer and activation of transcription (JAK/STAT) signalling pathway by IFNs leads to the upregulation of hundreds of interferon stimulated genes (ISGs) for which, many have the ability to rapidly kill viruses within infected cells. During the long course of evolution, viruses have evolved an extraordinary range of strategies to counteract the host immune responses in particular by targeting the JAK/STAT signalling pathway. Understanding how the IFN system is inhibited has provided critical insights into viral virulence and pathogenesis. Moreover, identification of factors encoded by viruses that modulate the JAK/STAT pathway has opened up opportunities to create new anti-viral drugs and rationally attenuated new generation vaccines, particularly for RNA viruses, by reverse genetics.

Similar source of differential blood mRNAs in lung cancer and pulmonary inflammatory diseases: calls for improved strategy for identifying cancer-specific biomarkers

BACKGROUND

Many studies try to identify cancer diagnostic biomarkers by comparing peripheral whole blood (PWB) of cancer samples and healthy controls, explicitly or implicitly assuming that such biomarkers are potential candidate biomarkers for distinguishing cancer from nonmalignant inflammation-associated diseases.

METHODS

Multiple PWB gene expression profiles for lung cancer/inflammation-associated pulmonary diseases were used for differential mRNAs identification and comparison and for proportion estimation of PWB cell subtypes.

RESULTS

The differentially expressed genes (DE genes) between lung cancer/inflammation-associated pulmonary patients and healthy controls were reproducibly identified in different datasets. For these DE genes observed in lung cancer/inflammation-associated pulmonary diseases, more than 90.2% were differentially expressed between myeloid cells and lymphoid cells, with at least 96.8% having consistent directions of regulation (up- or down-regulations) in myeloid cells compared to lymphoid cells, explainable by the shifted populations of PWB cell subtypes under the disease conditions. The comparison of DE genes for lung cancer and inflammation-associated pulmonary diseases showed that the overlapping genes were 100% consistent in the sense of direction of regulation.

CONCLUSIONS

The differential blood mRNAs observed in lung cancer and in inflammation-associated pulmonary diseases were similar, both mainly reflecting the difference between myeloid cells and lymphoid cells predominantly determined by PWB cell population shifts. Thus, the strategy of comparing cancer with healthy controls may provide little information of the ability of the identified candidate biomarkers in discriminating cancer from inflammation-associated pulmonary diseases.

Healing effect of a two-herb recipe (NF3) on foot ulcers in Chinese patients with diabetes: a randomized double-blind placebo-controlled study

BACKGROUND

In the present study, we examined the effect of a two-herb traditional Chinese medicine (NF3), comprised of Astragali Radix and Radix Rehmanniae, on the healing of diabetic foot ulcer and the possible molecular mechanisms involved.

METHODS

This was a prospective randomized double-blind placebo-controlled study. Sixteen diabetic patients were randomized to receive either placebo or NF3 for 6 months. Ulcer healing and sensory changes were examined. Molecular studies included measurement of serum tumor necrosis factor (TNF)-α and RNA microarray investigation.

RESULTS

The daily rate of reduction in ulcer area was 3.55% in the NF3 group and 1.52% in the placebo group (P = 0.062). In the index limb, the number of negative tests for sensory neuropathy using monofilament was reduced from 27% to 7% in the NF3 group and from 37% to 35% in the placebo group (P < 0.001). In addition, NF3 significantly decreased serum TNF-α levels (P = 0.034). Microarray studies revealed concerted changes following NF3 treatment in the expression of genes implicated in fibroblast regeneration, angiogenesis, and anti-inflammation.

CONCLUSIONS

In this proof-of-concept study, 6-month treatment with NF3 was associated with improved wound healing and sensation accompanied by concerted changes in gene expression.

Circulating Tumor Cells in Metastatic Breast Cancer: A Prognostic and Predictive Marker

The role of circulating tumor cells (CTCs) as a marker for disease progression in metastatic cancer is controversial. The current review will serve to summarize the evidence on CTCs as a marker of disease progression in patients with metastatic breast cancer. The immunohistochemistry(IHC)-based CellSearch^® is the only FDA-approved isolation technique for quantifying CTCs in patients with metastatic breast cancer. We searched PubMed and Web of Knowledge for clinical studies that assessed the prognostic and predictive value of CTCs using IHC-based isolation. The patient outcomes reported include median and Cox-proportional hazard ratios for overall-survival (OS) and progression-free-survival (PFS). All studies reported shorter OS for CTC-positive patients versus CTC-negative. A subset of the selected trials reported significant lower median PFS for CTC-positive patients. The reported trials support the utility of CTC enumeration for patient prognosis. But further studies are required to determine the utility of CTC enumeration for guiding patient therapy. There are three clinical trials ongoing to test this hypothesis. These studies, and others, will further establish the role of CTCs in clinical practice.

Hedgehog/GLI signaling activates suppressor of cytokine signaling 1 (SOCS1) in epidermal and neural tumor cells

Sustained hedgehog (Hh) signaling mediated by the GLI transcription factors is implicated in many types of cancer. Identification of Hh/GLI target genes modulating the activity of other pathways involved in tumor development promise to open new ways for better understanding of tumor development and maintenance. Here we show that SOCS1 is a direct target of Hh/GLI signaling in human keratinocytes and medulloblastoma cells. SOCS1 is a potent inhibitor of interferon gamma (IFN-y)/STAT1 signaling. IFN-у/STAT1 signaling can induce cell cycle arrest, apoptosis and anti-tumor immunity. The transcription factors GLI1 and GLI2 activate the SOCS1 promoter, which contains five putative GLI binding sites, and GLI2 binding to the promoter was shown by chromatin immunoprecipitation. Consistent with a role of GLI in SOCS1 regulation, STAT1 phosphorylation is reduced in cells with active Hh/GLI signaling and IFN-у/STAT1 target gene activation is decreased. Furthermore, IFN-у signaling is restored by shRNA mediated knock down of SOCS1. Here, we identify SOCS1 as a novel Hh/GLI target gene, indicating a negative role of Hh/GLI pathway in IFN-y/STAT1 signaling.

Imiquimod directly inhibits Hedgehog signalling by stimulating adenosine receptor/protein kinase A-mediated GLI phosphorylation

Imiquimod (IMQ), a nucleoside analogue of the imidazoquinoline family, is used in the topical treatment of basal cell carcinoma (BCC) and other skin diseases. It is reported to be a TLR7 and TLR8 agonist and, as such, initiates a Th1 immune response by activating sentinel cells in the vicinity of the tumour. BCC is a hedgehog (HH)-driven malignancy with oncogenic glioma-associated oncogene (GLI) signalling activated in a ligand-independent manner. Here we show that IMQ can also directly repress HH signalling by negatively modulating GLI activity in BCC and medulloblastoma cells. Further, we provide evidence that the repressive effect of IMQ on HH signalling is not dependent on TLR/MYD88 signalling. Our results suggest a mechanism for IMQ engaging adenosine receptors (ADORAs) to control GLI signalling. Pharmacological activation of ADORA with either an ADORA agonist or IMQ resulted in a protein kinase A (PKA)-mediated GLI phosphorylation and reduction in GLI activator levels. The activation of PKA and HH pathway target gene downregulation in response to IMQ were abrogated by ADORA inhibition. Furthermore, activated Smoothened signalling, which positively signals to GLI transcription factors, could be effectively counteracted by IMQ. These results reveal a previously unknown mode of action of IMQ in the treatment of BCC and also suggest a role for ADORAs in the regulation of oncogenic HH signalling.

Expression analysis of multiple myeloma CD138 negative progenitor cells using single molecule microarray readout

We present a highly sensitive bioanalytical microarray assay that enables the analysis of small genomic sample material. By combining an optimized cDNA purification step with single molecule cDNA detection on the microarray, the platform has improved sensitivity compared to conventional systems, allowing amplification-free determination of expression profiles with as little as 600ng total RNA. Total RNA from cells was reverse transcribed into fluorescently labeled cDNA and purified employing a precipitation method that minimizes loss of cDNA material. The microarray was scanned on a fluorescence chip-reader with single molecule sensitivity. Using the newly developed platform we were able to analyze the RNA expression profile of a subpopulation of rare multiple myeloma CD138 negative progenitor (MM CD138(neg)) cells. The high-sensitivity microarray approach led to the identification of a set of 20 genes differentially expressed in MM CD138(neg) cells. Our work demonstrates the applicability of a straight-forward single-molecule DNA array technology to current topics of molecular and cellular cancer research, which are otherwise difficult to address due to the limited amount of sample material.

Dichotomy in Hedgehog signaling between human healthy vessel and atherosclerotic plaques

The major cause for plaque instability in atherosclerotic disease is neoangiogenic revascularization, but the factors controlling this process remain only partly understood. Hedgehog (HH) is a morphogen with important functions in revascularization, but its function in human healthy vessel biology as well as in atherosclerotic plaques has not been well investigated. Hence, we determined the status of HH pathway activity both in healthy vessels and atherosclerotic plaques. A series of 10 healthy organ donor-derived human vessels, 17 coronary atherosclerotic plaques and 24 atherosclerotic carotid plaques were investigated for HH pathway activity. We show that a healthy vessel is characterized by a high level of HH pathway activity but that atherosclerotic plaques are devoid of HH signaling despite the presence of HH ligand in these pathological structures. Thus, a dichotomy between healthy vessels and atherosclerotic plaques with respect to the activation status of the HH pathway exists, and it is tempting to suggest that downregulation of HH signaling contributes to long-term plaque stability.

Gene expression signatures of radiation exposure in peripheral white blood cells of smokers and non-smokers

PURPOSE

The issue of potential confounding factors is critical to the development of any approach to radiation biodosimetry, and has not been fully addressed for gene expression-based approaches.

MATERIALS AND METHODS

As a step in this direction, we have investigated the effect of smoking on the global radiation gene expression response in ex vivo-irradiated peripheral blood cells using microarray analysis. We also evaluated the ability of gene expression signatures to predict the radiation exposure level of ex vivo-exposed samples from smokers and non-smokers of both genders.

RESULTS

We identified eight genes with a radiation response that was significantly affected by smoking status, and confirmed an effect of smoking on the radiation response of the four and a half LIM domains 2 (FHL2) gene using quantitative real-time polymerase chain reaction. The performance of our previously defined 74-gene signature in predicting the radiation dose to samples in this study was unaffected by differences in gender or smoking status, however, giving 98% correct prediction of dose category. This is the same accuracy as that found in the original study from which the signature was derived, using different donors.

CONCLUSION

The results support the development of peripheral blood gene expression as a viable strategy for radiation biodosimetry.

INTERRELATED TWO-WAY CLUSTERING AND ITS APPLICATION ON GENE EXPRESSION DATA

Microarray technologies are capable of simultaneously measuring the signals for thousands of messenger RNAs and large numbers of proteins from single samples. Arrays are now widely used in basic biomedical research for mRNA expression profiling and are increasingly being used to explore patterns of gene expression in clinical research. Most research has focused on the interpretation of the meaning of the microarray data which are transformed into gene expression matrices where usually the rows represent genes, the columns represent various samples. Clustering samples can be done by analyzing and eliminating of irrelevant genes. However, majority methods are supervised (or assisted by domain knowledge), less attention has been paid on unsupervised approaches which are important when little domain knowledge is available. In this paper, we present a new framework for unsupervised analysis of gene expression data, which applies an interrelated two-way clustering approach on the gene expression matrices. The goal of clustering is to identify important genes and perform cluster discovery on samples. The advantage of this approach is that we can dynamically manipulate the relationship between the gene clusters and sample groups while conducting an iterative clustering through both of them. The performance of the proposed method with various gene expression data sets is also illustrated.

Development and validation of a novel molecular biomarker diagnostic test for the early detection of sepsis

Introduction

Sepsis is a complex immunological response to infection characterized by early hyper-inflammation followed by severe and protracted immunosuppression, suggesting that a multi-marker approach has the greatest clinical utility for early detection, within a clinical environment focused on Systemic Inflammatory Response Syndrome (SIRS) differentiation. Pre-clinical research using an equine sepsis model identified a panel of gene expression biomarkers that define the early aberrant immune activation. Thus, the primary objective was to apply these gene expression biomarkers to distinguish patients with sepsis from those who had undergone major open surgery and had clinical outcomes consistent with systemic inflammation due to physical trauma and wound healing.

Methods

This was a multi-centre, prospective clinical trial conducted across four tertiary critical care settings in Australia. Sepsis patients were recruited if they met the 1992 Consensus Statement criteria and had clinical evidence of systemic infection based on microbiology diagnoses (n = 27). Participants in the post-surgical (PS) group were recruited pre-operatively and blood samples collected within 24 hours following surgery (n = 38). Healthy controls (HC) included hospital staff with no known concurrent illnesses (n = 20). Each participant had minimally 5 ml of PAXgene blood collected for leucocyte RNA isolation and gene expression analyses. Affymetrix array and multiplex tandem (MT)-PCR studies were conducted to evaluate transcriptional profiles in circulating white blood cells applying a set of 42 molecular markers that had been identified a priori. A LogitBoost algorithm was used to create a machine learning diagnostic rule to predict sepsis outcomes.

Results

Based on preliminary microarray analyses comparing HC and sepsis groups, a panel of 42-gene expression markers were identified that represented key innate and adaptive immune function, cell cycling, WBC differentiation, extracellular remodelling and immune modulation pathways. Comparisons against GEO data confirmed the definitive separation of the sepsis cohort. Quantitative PCR results suggest the capacity for this test to differentiate severe systemic inflammation from HC is 92%. The area under the curve (AUC) receiver operator characteristics (ROC) curve findings demonstrated sepsis prediction within a mixed inflammatory population, was between 86 and 92%.

Conclusions

This novel molecular biomarker test has a clinically relevant sensitivity and specificity profile, and has the capacity for early detection of sepsis via the monitoring of critical care patients.

Detection of the circulating tumor cells in cancer patients

As the presence of tumor cells circulating in the blood is associated with systemic disease and shortened survival, the establishment of a method to detect circulating tumor cells (CTCs) is of critical importance for a more concise staging and follow-up of cancer patients. Recently, the most robust strategies for the determination of CTCs are the PCR-based methods and the CellSearch® system that exploits the immunofluorescent characterization and isolation of cancer cells. Herein, we analyzed the experimental strategies used for determining CTCs with respect to accuracy, sensitivity and reproducibility in cancers of the breast, colon, prostate and melanoma.

Biomarkers in cancer micrometastasis: where are we at?

Despite considerable advances in the field of solid tumors, disseminated malignancy remains the cause of the vast majority of cancer-related deaths. In patients with no overt metastasis, early spread of tumor cells is usually undetected by current imaging technologies. In addition, the metastatic process is complex and depends on multiple interactions (crosstalk) of disseminating tumor cells with the individual homeostatic mechanisms, which the tumor cells can usurp. Despite these many variables, a flurry of surrogate biomarkers to detect micrometastasis has been developed in the last decade. These biomarkers open avenues for understanding cancer dormancy and metastasis, have the potential to provide novel therapeutic targets and may help predict outcome and therapeutic decisions at diagnosis and during follow-up of cancer patients. This review focuses on ongoing efforts to unravel metastasis biology, surrogate biomarkers currently investigated to monitor micrometastasis and tools used to identify, quantify and determine their capacity to efficiently establish metastasis.

Prediction of in vivo radiation dose status in radiotherapy patients using ex vivo and in vivo gene expression signatures

After a large-scale nuclear accident or an attack with an improvised nuclear device, rapid biodosimetry would be needed for triage. As a possible means to address this need, we previously defined a gene expression signature in human peripheral white blood cells irradiated ex vivo that predicts the level of radiation exposure with high accuracy. We now demonstrate this principle in vivo using blood from patients receiving total-body irradiation (TBI). Whole genome microarray analysis has identified genes responding significantly to in vivo radiation exposure in peripheral blood. A 3-nearest neighbor classifier built from the TBI patient data correctly predicted samples as exposed to 0, 1.25 or 3.75 Gy with 94% accuracy (P < 0.001) even when samples from healthy donor controls were included. The same samples were classified with 98% accuracy using a signature previously defined from ex vivo irradiation data. The samples could also be classified as exposed or not exposed with 100% accuracy. The demonstration that ex vivo irradiation is an appropriate model that can provide meaningful prediction of in vivo exposure levels, and that the signatures are robust across diverse disease states and independent sample sets, is an important advance in the application of gene expression for biodosimetry.

The pursuit of oncotargets through understanding defective cell regulation

More effective anticancer agents are essential, as has too often been demonstrated by the paucity of therapeutics which preserve life. Their discovery is very difficult. Many approaches are being applied, from testing folk medicines to automated high throughput screening of large chemical libraries. Mutations in cancer cells create dysfunctional regulatory systems. This Perspective summarizes an approach to applying defective molecular control mechanisms as oncotargets on which drug discoveries against cancer can be based.

The pursuit of oncotargets through understanding defective cell regulation

More effective anticancer agents are essential, as has too often been demonstrated by the paucity of therapeutics which preserve life. Their discovery is very difficult. Many approaches are being applied, from testing folk medicines to automated high throughput screening of large chemical libraries. Mutations in cancer cells create dysfunctional regulatory systems. This Perspective summarizes an approach to applying defective molecular control mechanisms as oncotargets on which drug discoveries against cancer can be based.

Gene expression profiling in whole blood of patients with coronary artery disease

Owing to the dynamic nature of the transcriptome, gene expression profiling is a promising tool for discovery of disease-related genes and biological pathways. In the present study, we examined gene expression in whole blood of 12 patients with CAD (coronary artery disease) and 12 healthy control subjects. Furthermore, ten patients with CAD underwent whole-blood gene expression analysis before and after the completion of a cardiac rehabilitation programme following surgical coronary revascularization. mRNA and miRNA (microRNA) were isolated for expression profiling. Gene expression analysis identified 365 differentially expressed genes in patients with CAD compared with healthy controls (175 up- and 190 down-regulated in CAD), and 645 in CAD rehabilitation patients (196 up- and 449 down-regulated post-rehabilitation). Biological pathway analysis identified a number of canonical pathways, including oxidative phosphorylation and mitochondrial function, as being significantly and consistently modulated across the groups. Analysis of miRNA expression revealed a number of differentially expressed miRNAs, including hsa-miR-140-3p (control compared with CAD, P=0.017), hsa-miR-182 (control compared with CAD, P=0.093), hsa-miR-92a and hsa-miR-92b (post- compared with pre-exercise, P<0.01). Global analysis of predicted miRNA targets found significantly reduced expression of genes with target regions compared with those without: hsa-miR-140-3p (P=0.002), hsa-miR-182 (P=0.001), hsa-miR-92a and hsa-miR-92b (P=2.2×10⁻¹⁶). In conclusion, using whole blood as a ‘surrogate tissue’ in patients with CAD, we have identified differentially expressed miRNAs, differentially regulated genes and modulated pathways which warrant further investigation in the setting of cardiovascular function. This approach may represent a novel non-invasive strategy to unravel potentially modifiable pathways and possible therapeutic targets in cardiovascular disease.

Relation of platelet and leukocyte inflammatory transcripts to body mass index in the Framingham heart study

BACKGROUND

Although many genetic epidemiology and biomarker studies have been conducted to examine associations of genetic variants and circulating proteins with cardiovascular disease and risk factors, there has been little study of gene expression or transcriptomics. Quantitative differences in the abundance of transcripts has been demonstrated in malignancies, but gene expression from a large community-based cohort examining risk of cardiovascular disease has never been reported.

METHODS AND RESULTS

On the basis of preliminary microarray data and previously suggested genes from the literature, we measured expression of 48 genes by high-throughput quantitative reverse-transcriptase polymerase chain reaction in 1846 participants of the Framingham Offspring cohort from RNA derived from isolated platelets and leukocytes. A multivariable stepwise regression model was used to assess clinical correlates of quantitative RNA expression. For specific inflammatory platelet-derived transcripts, including ICAM1, IFNG, IL1R1, IL6, MPO, COX2, TNF, TLR2, and TLR4, there were significant associations with higher body mass index (BMI). Compared with platelets, fewer leukocyte-derived transcripts were associated with BMI or other cardiovascular risk factors. Select transcripts were found to be highly heritable, including GPIBA and COX1. Almost uniformly, heritable transcripts were not those associated with BMI.

CONCLUSIONS

Inflammatory transcripts derived from platelets, particularly those part of the nuclear factor kappa B pathway, are associated with BMI, whereas others are heritable. This is the first study, using a large community-based cohort, to demonstrate clinical correlates of gene expression and is consistent with the hypothesis that specific peripheral-blood transcripts play a role in the pathogenesis of coronary heart disease and its risk factors.

Assessing the human immune system through blood transcriptomics

Blood is the pipeline of the immune system. Assessing changes in transcript abundance in blood on a genome-wide scale affords a comprehensive view of the status of the immune system in health and disease. This review summarizes the work that has used this approach to identify therapeutic targets and biomarker signatures in the field of autoimmunity and infectious disease. Recent technological and methodological advances that will carry the blood transcriptome research field forward are also discussed.

A need for basic research on fluid-based early detection biomarkers

Cancer continues to be a major cause of mortality despite decades of effort and expense. The problem reviewed here is that before many cancers are discovered they have already progressed to become drug resistant or metastatic. Biomarkers found in blood or other body fluids could supplement current clinical indicators to permit earlier detection and thereby reduce cancer mortality.

Clinical utility of circulating tumor cells: a role for monitoring response to therapy and drug development

Detection of circulating tumor cells (CTCs) and circulating endothelial cells (CECs) have been described in a variety of solid tumors including breast, prostate, gastric, colorectal cancers and melanoma. Several studies have demonstrated that increased numbers of such CTCs are predictive of worse outcome in early-stage disease as well as decreased progression-free survival and overall survival in advanced stages. It is well known that malignancies comprise heterogeneous populations of cells. Therefore, CTCs and CECs may represent the most relevant tumor population - the tumor cell population most likely to metastasize. Recently, technical advances have rendered this population to be more easily accessible to both researchers and clinicians. As CTCs and CECs have become easier to repeatedly sample with a high degree of accuracy, these cells represent an attractive surrogate marker of the primary tumor. Studies have shown that CTCs and CECs can be phenotypically and genotypically compared with the primary tumor and are faithful representatives; and where phenotypic differences exist, such phenotypes can be exploited for selecting molecularly targeted therapies. Therefore, CTC and CEC enumeration and analysis represent a clinically meaningful tool for assessing prognosis, monitoring response to therapy, pharmacodynamic studies and rational selection of therapies in cancer patients.

The biological information obtainable from circulating tumor cells

The reliable detection of circulating tumor cells (CTCs) in metastatic breast cancer (MBC) is possible by using immunomagnetic separation and subsequent characterization with the CellSpotter analyzer (Veridex LLC, a Johnson & Johnson company, Warren, NJ, USA). This technology is becoming a standard tool for the 'real-time' assessment of prognosis and response to treatment. The prognostic value is independent of the line of therapy (e.g. first-line versus second-line or more), site of metastasis (e.g. visceral versus soft tissue/bone), and subtype of disease (e.g. basal vs. luminal). Moreover, CTCs detection has been recently associated with worse outcome also in patients with primary breast cancer that have completed neoadjuvant or adjuvant therapy. These findings suggest the need to further investigate the biology of CTCs. Several investigators have recently focused on determining the feasibility of performing the genotypic characterization of CTCs and correlate it with the expression of similar genes in primary or metastatic lesions. Some of the studies have used a recently introduced detection technology combining EpCAM-enrichment and PCR analysis (AdnaTest Breast Cancer, Adnagen AG, Germany). The studies seem to indicate that CTCs differ in the expression of hormone receptors and HER-2 compared to primary disease. Furthermore, some of the phenotypic assessment seems to suggest that a fraction of CTCs could be identified as cancer stem cells. Those data suggest interesting observations in the biology of those cells and indicate the possibility to evaluate targeted therapies based on the genomic profiling of CTCs, particularly with regards to HER-2 determination.

Gene expression profiles of HIV-1-infected glia and brain: toward better understanding of the role of astrocytes in HIV-1-associated neurocognitive disorders

Astrocytes are the major cellular component of the central nervous system (CNS), and they play multiple roles in brain development, normal brain function, and CNS responses to pathogens and injury. The functional versatility of astrocytes is linked to their ability to respond to a wide array of biological stimuli through finely orchestrated changes in cellular gene expression. Dysregulation of gene expression programs, generally by chronic exposure to pathogenic stimuli, may lead to dysfunction of astrocytes and contribute to neuropathogenesis. Here, we review studies that employ functional genomics to characterize the effects of HIV-1 and viral pathogenic proteins on cellular gene expression in astrocytes in vitro. We also present the first microarray analysis of primary mouse astrocytes exposed to HIV-1 in culture. In spite of different experimental conditions and microarray platforms used, comparison of the astrocyte array data sets reveals several common gene-regulatory changes that may underlie responses of these cells to HIV-1 and its proteins. We also compared the transcriptional profiles of astrocytes with those obtained in analyses of brain tissues of patients with HIV-1 dementia and macaques infected with simian immunodeficiency virus (SIV). Notably, many of the gene characteristics of responses to HIV-1 in cultured astrocytes were also altered in HIV-1 or SIV-infected brains. Functional genomics, in conjunction with other approaches, may help clarify the role of astrocytes in HIV-1 neuropathogenesis.

Type I interferon-sensitive recombinant newcastle disease virus for oncolytic virotherapy

Newcastle disease virus (NDV), an avian paramyxovirus, is tumor selective and intrinsically oncolytic because of its potent ability to induce apoptosis. Several studies have demonstrated that NDV is selectively cytotoxic to tumor cells but not normal cells due to defects in the interferon (IFN) antiviral responses of tumor cells. Many naturally occurring strains of NDV have an intact IFN-antagonistic function and can still replicate in normal human cells. To avoid potential toxicity issues with NDV, especially in cancer patients with immunosuppression, safe NDV-oncolytic vectors are needed. We compared the cell killing abilities of (i) a recombinant NDV (rNDV) strain, Beaudette C, containing an IFN-antagonistic, wild-type V protein (rBC), (ii) an isogenic recombinant virus with a mutant V protein (rBC-Edit virus) that induces increased IFN in infected cells and whose replication is restricted in normal human cells, and (iii) a recombinant LaSota virus with a virulent F protein cleavage site that is as interferon sensitive as rBC-Edit virus (LaSota V.F. virus). Our results indicated that the tumor-selective replication of rNDV is determined by the differential regulation of IFN-alpha and downstream antiviral genes induced by IFN-alpha, especially through the IRF-7 pathway. In a nude mouse model of human fibrosarcoma, we show that the IFN-sensitive NDV variants are as effective as IFN-resistant rBC virus in clearing the tumor burden. In addition, mice treated with rNDV exhibited no signs of toxicity to the viruses. These findings indicate that augmentation of innate immune responses by NDV results in selective oncolysis and offer a novel and safe virotherapy platform.

A practical platform for blood biomarker study by using global gene expression profiling of peripheral whole blood

Background

Although microarray technology has become the most common method for studying global gene expression, a plethora of technical factors across the experiment contribute to the variable of genome gene expression profiling using peripheral whole blood. A practical platform needs to be established in order to obtain reliable and reproducible data to meet clinical requirements for biomarker study.

Methods and Findings

We applied peripheral whole blood samples with globin reduction and performed genome-wide transcriptome analysis using Illumina BeadChips. Real-time PCR was subsequently used to evaluate the quality of array data and elucidate the mode in which hemoglobin interferes in gene expression profiling.

We demonstrated that, when applied in the context of standard microarray processing procedures, globin reduction results in a consistent and significant increase in the quality of beadarray data. When compared to their pre-globin reduction counterparts, post-globin reduction samples show improved detection statistics, lowered variance and increased sensitivity. More importantly, gender gene separation is remarkably clearer in post-globin reduction samples than in pre-globin reduction samples. Our study suggests that the poor data obtained from pre-globin reduction samples is the result of the high concentration of hemoglobin derived from red blood cells either interfering with target mRNA binding or giving the pseudo binding background signal.

Conclusion

We therefore recommend the combination of performing globin mRNA reduction in peripheral whole blood samples and hybridizing on Illumina BeadChips as the practical approach for biomarker study.

Cooperation between GLI and JUN enhances transcription of JUN and selected GLI target genes

Sustained Hedgehog (HH) signaling is implicated in basal cell carcinoma of the skin and other types of cancer. Here we show that GLI1 and GLI2, the main transcriptional activators of the HH pathway, directly regulate expression of the activator protein 1 (AP-1) family member JUN, a transcription factor controlling keratinocyte proliferation and skin homeostasis. Activation of the JUN promoter by GLI is dependent on a GLI-binding site and the AP-1 sites known to be involved in self-activation of JUN. Transcription of JUN is greatly enhanced in the presence of GLI and requires activated JUN protein. GLI2act is a more potent activator than GLI1 in these experiments and physical interaction with phosphorylated JUN was only detected for GLI2act. The synergistic effect of GLI and JUN extends to the activation of further GLI target genes as shown by shRNA-mediated knockdown of JUN in human keratinocytes. Some of these cooperatively activated genes are involved in cell-cycle progression, which is consistent with a significant reduction of the proliferative potential of GLI in the absence of JUN. These results suggest a novel connection between HH/GLI pathway activity and JUN, which may contribute to the oncogenic activity of HH/GLI signaling in skin.

The six family of homeobox genes in development and cancer

The homeobox gene superfamily encodes transcription factors that act as master regulators of development through their ability to activate or repress a diverse range of downstream target genes. Numerous families exist within the homeobox gene superfamily, and are classified on the basis of conservation of their homeodomains as well as additional motifs that contribute to DNA binding and to interactions with other proteins. Members of one such family, the Six family, form a transcriptional complex with Eya and Dach proteins, and together these proteins make up part of the retinal determination network first identified in Drosophila. This network is highly conserved in both invertebrate and vertebrate species, where it influences the development of numerous organs in addition to the eye, primarily through regulation of cell proliferation, survival, migration, and invasion. Mutations in Six, Eya, and Dach genes have been identified in a variety of human genetic disorders, demonstrating their critical role in human development. In addition, aberrant expression of Six, Eya, and Dach occurs in numerous human tumors, and Six1, in particular, plays a causal role both in tumor initiation and in metastasis. Emerging evidence for the importance of Six family members and their cofactors in numerous human tumors suggests that targeting of this complex may be a novel and powerful means to inhibit both tumor growth and progression.

Diagnostic mRNA expression patterns of inflamed, benign, and malignant colorectal biopsy specimen and their correlation with peripheral blood results

PURPOSE

Gene expression profile (GEP)-based classification of colonic diseases is a new method for diagnostic purposes. Our aim was to develop diagnostic mRNA expression patterns that may establish the basis of a new molecular biological diagnostic method.

EXPERIMENTAL DESIGN

Total RNA was extracted, amplified, and biotinylated from frozen colonic biopsies of patients with colorectal cancer (n=22), adenoma (n=20), hyperplastic polyp (n=11), inflammatory bowel disease (n=21), and healthy normal controls (n=11), as well as peripheral blood samples of 19 colorectal cancer and 11 healthy patients. Genome-wide gene expression profile was evaluated by HGU133plus2 microarrays. To identify the differentially expressed features, the significance analysis of microarrays and, for classification, the prediction analysis of microarrays were used. Expression patterns were validated by real-time PCR. Tissue microarray immunohistochemistries were done on tissue samples of 121 patients.

RESULTS

Adenoma samples could be distinguished from hyperplastic polyps by the expression levels of nine genes including ATP-binding cassette family A, member 8, insulin-like growth factor 1 and glucagon (sensitivity, 100%; specificity, 90.91%). Between low-grade and high-grade dysplastic adenomas, 65 classifier probesets such as aquaporin 1, CXCL10, and APOD (90.91/100) were identified; between colorectal cancer and adenoma, 61 classifier probesets including axin 2, von Willebrand factor, tensin 1, and gremlin 1 (90.91/100) were identified. Early- and advanced-stage colorectal carcinomas could be distinguished using 34 discriminatory transcripts (100/66.67).

CONCLUSIONS

Whole genomic microarray analysis using routine biopsy samples is suitable for the identification of discriminative signatures for differential diagnostic purposes. Our results may be the basis for new GEP-based diagnostic methods.

Gene expression signatures of radiation response are specific, durable and accurate in mice and humans

BACKGROUND

Previous work has demonstrated the potential for peripheral blood (PB) gene expression profiling for the detection of disease or environmental exposures.

METHODS AND FINDINGS

We have sought to determine the impact of several variables on the PB gene expression profile of an environmental exposure, ionizing radiation, and to determine the specificity of the PB signature of radiation versus other genotoxic stresses. Neither genotype differences nor the time of PB sampling caused any lessening of the accuracy of PB signatures to predict radiation exposure, but sex difference did influence the accuracy of the prediction of radiation exposure at the lowest level (50 cGy). A PB signature of sepsis was also generated and both the PB signature of radiation and the PB signature of sepsis were found to be 100% specific at distinguishing irradiated from septic animals. We also identified human PB signatures of radiation exposure and chemotherapy treatment which distinguished irradiated patients and chemotherapy-treated individuals within a heterogeneous population with accuracies of 90% and 81%, respectively.

CONCLUSIONS

We conclude that PB gene expression profiles can be identified in mice and humans that are accurate in predicting medical conditions, are specific to each condition and remain highly accurate over time.

GLI2-specific transcriptional activation of the bone morphogenetic protein/activin antagonist follistatin in human epidermal cells

Hedgehog (HH) signaling in the epidermis is primarily mediated by the zinc finger transcription factors GLI1 and GLI2. Exquisite regulation of HH/GLI signaling is crucial for proper specification of the epidermal lineage and development of its derivatives, whereas dysregulation of HH/GLI signaling disrupts tissue homeostasis and causes basal cell carcinoma (BCC). Similarly, bone morphogenetic proteins (BMPs) and activins have been described as key signaling factors in the complex regulation of epidermal fate decisions, although their precise interplay with HH/GLI is largely elusive. Here we show that, in human epidermal cells, expression of the activin/BMP antagonist follistatin (FST) is predominantly up-regulated by the HH effector GLI2. Consistently, we found strong FST expression in the outer root sheath of human hair follicles and BCC. Detailed promoter analysis showed that two sequences with homology to the GLI consensus binding site are required for GLI2-mediated activation. Interestingly, activation of the FST promoter is highly GLI2-specific, because neither GLI1 nor GLI3 can significantly increase FST transcription. GLI2 specificity requires the presence of a 518-bp fragment in the proximal FST promoter region. On the protein level, sequences C-terminal to the zinc finger are responsible for GLI2-specific activation of FST transcription, pointing to the existence of GLI-interacting cofactors that modulate GLI target specificity. Our results reveal a key role of GLI2 in activation of the activin/BMP antagonist FST in response to HH signaling and provide new evidence for a regulatory interaction between HH and activin/BMP signaling in hair follicle development and BCC.

Expression profiling of vitamin D treated primary human keratinocytes

Vitamin D has attracted much attention by its ability to stop cell proliferation and induce differentiation, which became of particular interest for the treatment of cancer and psoriasis. We performed an expression profile of 12 hours and 24 hours 1alpha,25-dihydroxyvitamin D(3) (1alpha,25(OH)(2)D(3)) treated primary human keratinocytes, to determine the changes in gene expression induced by the steroid in order to improve our understanding of the biological activity of 1alpha,25(OH)(2)D(3). This we expect to be useful for establishing a test system for vitamin D analogs or might open new therapeutic targets or uses for the hormone. For the filter array experiments a non-redundant set of 2135 sequence verified EST clones was used. The normalized raw data of 2 filters per time point were combined and subjected to SAM analysis to further increase the statistical significance. 86 positive and 50 negative genes were identified after 12 h. The numbers went down to 43 positive and 1 negative gene after 24 h of treatment. Fifteen genes are up-regulated over a longer period of time (12 h and 24 h). Results were verified by real-time PCR and/or Northern blots. Targets identified are involved in intracellular signaling, transcription, cell cycle, metabolism, cellular growth, constitution of the extracellular matrix or the cytoskeleton and apoptosis, immune responses, and DNA repair, respectively. Expression profiles showed an initial stop of proliferation and induction of differentiation, and resumed proliferation after prolonged incubation, most likely due to degradation of the hormone.

Evaluation and significance of circulating epithelial cells in patients with hormone-refractory prostate cancer

OBJECTIVE

To determine the feasibility of using flow cytometry fluorescence-activated cell sorting (FACS) analysis for detecting circulating epithelial cells (CECs) in patients with hormone-refractory prostate cancer (HRPC), and to determine whether CECs can be used to predict survival in these patients.

PATIENTS AND METHODS

Several prognostic models that include routinely used clinical and laboratory variables for predicting survival in men with HRPC have been reported; the presence of CECs measured by reverse transcriptase-polymerase chain reaction for prostate-specific antigen (PSA) in patients with HRPC is an independent prognostic factor for survival. CECs detected by FACS analysis correlate with advanced stage and poor survival outcome. A retrospective study was conducted to assess the presence of CECs by FACS analysis in metastatic HRPC patients initiating systemic chemotherapy with a taxane-based regimen. The association between clinical variables previously described and the presence of CECs along with the effect of the magnitude of CECs on survival was calculated, in 41 patients with HRPC, all of whom had peripheral blood collected for FACS analysis.

RESULTS

Except for four patients, all those with metastatic HRPC had detectable CECs. Among these patients, the number of CECs/mL was correlated with age, serum PSA level and serum alkaline phosphatase (ALP). Higher serum levels of PSA and ALP predicted a poor survival outcome. Similarly, patients with < or =1.8 CECs/mL had a significantly longer survival than those with more CECs/mL (P = 0.02). With a median follow-up of 15.4 months, the median overall survival for all patients was 18.4 months.

CONCLUSIONS

The presence of more CECs in patients with metastatic HRPC was associated with a poorer survival outcome; levels of > or =1.8 CECs/mL were associated with a shorter survival in patients with metastatic HRPC.

Molecular biomarkers for cancer detection in blood and bodily fluids

Cancer is a major and increasing public health problem worldwide. Traditionally, the diagnosis and staging of cancer, as well as the evaluation of response to therapy have been primarily based on morphology, with relatively few cancer biomarkers currently in use. Conventional biomarker studies have been focused on single genes or discrete pathways, but this approach has had limited success because of the complex and heterogeneous nature of many cancers. The completion of the human genome project and the development of new technologies have greatly facilitated the identification of biomarkers for assessment of cancer risk, early detection of primary cancers, monitoring cancer treatment, and detection of recurrence. This article reviews the various approaches used for development of such markers and describes markers of potential clinical interest in major types of cancer. Finally, we discuss the reasons why so few cancer biomarkers are currently available for clinical use.

Identification of prostate cancer mRNA markers by averaged differential expression and their detection in biopsies, blood, and urine

The advent of serum prostate-specific antigen (PSA) as a biomarker has enabled early detection of prostate cancer and, hence, improved clinical outcome. However, a low PSA is not a guarantee of disease-free status, and an elevated PSA is frequently associated with a negative biopsy. Therefore, our goal is to identify molecular markers that can detect prostate cancer with greater specificity in body fluids such as urine or blood. We used the RT-PCR differential display method to first identify mRNA transcripts differentially expressed in tumor vs. patient-matched nontumor prostate tissue. This analysis led to the identification of 44 mRNA transcripts that were expressed differentially in some but not all tumor specimens examined. To identify mRNA transcripts that are differentially expressed in most tumor specimens, we turned to differential display of pooled tissue samples, a technique we name averaged differential expression (ADE). We performed differential display of mRNA from patient-matched nontumor vs. tumor tissue, each pooled from 10 patients with various Gleason scores. Differentially expressed mRNA transcripts identified by ADE were fewer in number, but were expressed in a greater percentage of tumors (>75%) than those identified by differential display of mRNA from individual patient samples. Differential expression of these mRNA transcripts was also detected by RT-PCR in mRNA isolated from urine and blood samples of prostate cancer patients. Our findings demonstrate the principle that specific cDNA probes of frequently differentially expressed mRNA transcripts identified by ADE can be used for the detection of prostate cancer in urine and blood samples.

Microarray-based identification and RT-PCR test screening for epithelial-specific mRNAs in peripheral blood of patients with colon cancer

BACKGROUND

The efficacy of screening for colorectal cancer using a simple blood-based assay for the detection of tumor cells disseminated in the circulation at an early stage of the disease is gaining positive feedback from several lines of research. This method seems able to reduce colorectal cancer mortality and may replace colonoscopy as the most effective means of detecting colonic lesions.

METHODS

In this work, we present a new microarray-based high-throughput screening method to identifying candidate marker mRNAs for the early detection of epithelial cells diluted in peripheral blood cells. This method includes 1. direct comparison of different samples of colonic mucosa and of blood cells to identify consistent epithelial-specific mRNAs from among 20,000 cDNA assayed by microarray slides; 2. identification of candidate marker mRNAs by data analysis, which allowed selection of only 10 putative differentially expressed genes; 3. Selection of some of the most suitable mRNAs (TMEM69, RANBP3 and PRSS22) that were assayed in blood samples from normal subjects and patients with colon cancer as possible markers for the presence of epithelial cells in the blood, using reverse transcription-polymerase chain reaction (RT-PCR).

RESULTS

Our present results seem to provide an indication, for the first time obtained by genome-scale screening, that a suitable and consistent colon epithelium mRNA marker may be difficult to identify.

CONCLUSION

The design of new approaches to identify such markers is warranted.

Gene expression signature in organized and growth-arrested mammary acini predicts good outcome in breast cancer

Nonmalignant human mammary epithelial cells (HMEC) seeded in laminin-rich extracellular matrix (lrECM) form polarized acini and, in doing so, transit from a disorganized proliferating state to an organized growth-arrested state. We hypothesized that the gene expression pattern of organized and growth-arrested HMECs would share similarities with breast tumors with good prognoses. Using Affymetrix HG-U133A microarrays, we analyzed the expression of 22,283 gene transcripts in 184 (finite life span) and HMT3522 S1 (immortal nonmalignant) HMECs on successive days after seeding in a lrECM assay. Both HMECs underwent growth arrest in G0-G1 and differentiated into polarized acini between days 5 and 7. We identified gene expression changes with the same temporal pattern in both lines and examined the expression of these genes in a previously published panel of microarray data for 295 breast cancer samples. We show that genes that are significantly lower in the organized, growth-arrested HMEC than in their proliferating counterparts can be used to classify breast cancer patients into poor and good prognosis groups with high accuracy. This study represents a novel unsupervised approach to identifying breast cancer markers that may be of use clinically.

Prognostic Significance of Disseminated Tumor Cells as Detected by Quantitative Real-Time Reverse-Transcriptase Polymerase Chain Reaction in Patients with Breast Cancer

BACKGROUND

In this study we have validated the feasibility of detecting disseminated tumor cells (DTC) by real-time reverse-transcriptase polymerase chain reaction (RT-PCR) analysis. Bone marrow samples from a large cohort of patients with breast cancer were analyzed for the presence of DTC by immunocytochemistry (ICC) or a molecular-based method.

PATIENTS AND METHODS

Bone marrow samples were collected from 170 patients with breast cancer with stage I-IV disease before the initiation of any local or systemic treatment. Staining for cytokeratin (CK)-positive cells was performed with the Epimet kit. Disseminated tumor cells were also quantified by measuring relative gene expression for CK19 and mammaglobin (MAM) using a quantitative RT-PCR detection method. The mean follow-up time was 30 months. Kaplan-Meier analysis was used for predicting overall survival.

RESULTS

Despite an excellent quantitative correlation and qualitative concordance between ICC and RT-PCR, survival analysis suggested an improved prognostic significance of DTC as detected by quantitative RT-PCR. Univariate survival analysis computed a relative risk of death of 2.87 for women with ICC-positive cells in the bone marrow, as compared with those without positive cells. The relative risk for women with RT-PCR-positive bone marrow was even higher: 3.5 (CK19) and 3.39 (MAM). In multivariate analysis, bone marrow CK19 was a stronger prognostic factor than bone marrow ICC.

CONCLUSION

Reverse-transcriptase polymerase chain reaction-detected DTC is shown to be prognostically significant in untreated patients with breast cancer. Furthermore, it seems to be a more sensitive method for detecting DTC in bone marrow samples when compared with ICC.

Benchmarking a memetic algorithm for ordering microarray data

This work introduces a new algorithm for "gene ordering". Given a matrix of gene expression data values, the task is to find a permutation of the gene names list such that genes with similar expression patterns should be relatively close in the permutation. The algorithm is based on a combined approach that integrates a constructive heuristic with evolutionary and Tabu Search techniques in a single methodology. To evaluate the benefits of this method, we compared our results with the current outputs provided by several widely used algorithms in functional genomics. We also compared the results with our own hierarchical clustering method when used in isolation. We show that the use of images, corrupted with known levels of noise, helps to illustrate some aspects of the performance of the algorithms and provide a complementary benchmark for the analysis. The use of these images, with known high-quality solutions, facilitates in some cases the assessment of the methods and helps the software development, validation and reproducibility of results. We also propose two quantitative measures of performance for gene ordering. Using these measures, we make a comparison with probably the most used algorithm (due to Eisen and collaborators, PNAS 1998) using a microarray dataset available on the public domain (the complete yeast cell cycle dataset).