Kinase substrate protein microarray analysis of human colon cancer and hepatic metastasis

BACKGROUND

Liver metastases represent the major determinant of survival in patients with colorectal cancer (CRC). In cases with unresectable liver disease, more effective agents are needed, since chemotherapy achieves median survival of only 15 months. Protein kinases coordinate complex functions that are often disregulated in cancer and are therefore considered important targets for molecular therapeutics. In this study, we investigated the phosphoproteomic status of different protein kinases in primary CRC and in liver metastases.

METHODS

The status of 29 key endpoints was evaluated using reverse phase protein array on laser capture microdissected neoplastic cells from five primary CRCs without metastases, three patient-matched primary CRCs and synchronous liver metastases and five CRC metachronous liver metastases.

RESULTS

Unsupervised hierarchical two-way clustering analysis showed an entirely different phosphoproteomic profile in primary CRCs compared to liver metastases. This difference was observed also in primary and metastatic patient-matched lesions.

CONCLUSIONS

Our findings of different signaling pathways between primary and metastatic CRC suggest a possible microenvironment effect, and emphasize the need to perform molecular network analysis of metastatic tissue when molecular targeting is considered.

A nondestructive molecule extraction method allowing morphological and molecular analyses using a single tissue section

In clinical practice, molecular analysis of tumor specimens is often restricted by available technology for sample preparation. Virtually all current methods require homogenization of tissues for molecule extraction. We have developed a simple, rapid, nondestructive molecule extraction (NDME) method to extract proteins and nucleic acids directly from a single fixed or frozen tissue section without destroying the tissue morphology. The NDME method is based upon exposure of micron-thick tissue section to extraction buffer with the help of heating and/or intact physical forces (ultrasound and microwave) to facilitate release of macromolecules into the buffer. The extracted proteins and nucleic acids can be used directly without further purification for downstream SDS-PAGE analysis, immunoblotting, protein array, mass spectra protein profiling, PCR, and RT-PCR reactions. Most importantly, the NDME procedure also serves as an antigen retrieval treatment, so that after NDME, the same tissue section can be used for histopathological analyses, such as H&E staining, immunohistochemistry, and in situ hybridization. Thus, the NDME method allows, for the first time, both histological diagnosis and molecular analysis on a single tissue section, whether it is from frozen or fixed tissue specimens.

SELDI-TOF mass spectrometry for cancer biomarker discovery and serum proteomic diagnostics

Proteomics is more than the identification of proteins that are altered in expression as a consequence of disease. Among the tools critical for the detection, treatment and monitoring of disease are biomarkers. The necessity for new methods to identify and validate biomarkers is underscored by the increased survival of patients diagnosed at early stages of cancer. Serum proteomic pattern diagnostics is a new technique in which proteomic signatures are used as a diagnostic classifier. Surface-enhanced laser desorption/ionization time-of-flight mass spectrometry has shown promise as a modality for biomarker discovery of early-stage cancers. Mass spectrometry-derived protein signatures have been modeled and are now moving into validation. Further sequencing of these key features can lead to new insights into disease etiology and intervention.

Adipocyte-derived collagen VI affects early mammary tumor progression in vivo, demonstrating a critical interaction in the tumor/stroma microenvironment

The interactions of transformed cells with the surrounding stromal cells are of importance for tumor progression and metastasis. The relevance of adipocyte-derived factors to breast cancer cell survival and growth is well established. However, it remains unknown which specific adipocyte-derived factors are most critical in this process. Collagen VI is abundantly expressed in adipocytes. Collagen(-/-) mice in the background of the mouse mammary tumor virus/polyoma virus middle T oncogene (MMTV-PyMT) mammary cancer model demonstrate dramatically reduced rates of early hyperplasia and primary tumor growth. Collagen VI promotes its growth-stimulatory and pro-survival effects in part by signaling through the NG2/chondroitin sulfate proteoglycan receptor expressed on the surface of malignant ductal epithelial cells to sequentially activate Akt and beta-catenin and stabilize cyclin D1. Levels of the carboxyterminal domain of collagen VIalpha3, a proteolytic product of the full-length molecule, are dramatically upregulated in murine and human breast cancer lesions. The same fragment exerts potent growth-stimulatory effects on MCF-7 cells in vitro. Therefore, adipocytes play a vital role in defining the ECM environment for normal and tumor-derived ductal epithelial cells and contribute significantly to tumor growth at early stages through secretion and processing of collagen VI.

Adipocyte-derived collagen VI affects early mammary tumor progression in vivo, demonstrating a critical interaction in the tumor/stroma microenvironment

The interactions of transformed cells with the surrounding stromal cells are of importance for tumor progression and metastasis. The relevance of adipocyte-derived factors to breast cancer cell survival and growth is well established. However, it remains unknown which specific adipocyte-derived factors are most critical in this process. Collagen VI is abundantly expressed in adipocytes. Collagen(-/-) mice in the background of the mouse mammary tumor virus/polyoma virus middle T oncogene (MMTV-PyMT) mammary cancer model demonstrate dramatically reduced rates of early hyperplasia and primary tumor growth. Collagen VI promotes its growth-stimulatory and pro-survival effects in part by signaling through the NG2/chondroitin sulfate proteoglycan receptor expressed on the surface of malignant ductal epithelial cells to sequentially activate Akt and beta-catenin and stabilize cyclin D1. Levels of the carboxyterminal domain of collagen VIalpha3, a proteolytic product of the full-length molecule, are dramatically upregulated in murine and human breast cancer lesions. The same fragment exerts potent growth-stimulatory effects on MCF-7 cells in vitro. Therefore, adipocytes play a vital role in defining the ECM environment for normal and tumor-derived ductal epithelial cells and contribute significantly to tumor growth at early stages through secretion and processing of collagen VI.

Genomic and proteomic technologies for individualisation and improvement of cancer treatment

The development of microarray-based technologies for characterising tumours, both at the genomic and proteomic levels, has had a significant impact on the field of oncology. Gene expression profiling of various human tumour tissues has led to the identification of expression patterns related to disease outcome and drug resistance, as well as to the discovery of new therapeutic targets and insights into disease pathogenesis. Protein microarray technologies, such as reverse-phase protein arrays, provide the unique opportunity to profile tissues and assess the activity of signalling pathways within isolated cell populations. This technology can be used to identify patients likely to benefit from specific treatment modalities and also to monitor therapeutic response in samples obtained during and after treatment. Routine application of genomic and proteomic microarray technologies in clinical practice will require significant efforts to standardise the techniques, controls and reference standards, and analytical tools used. Extensive, independent validation using large, statistically-powered datasets will also be necessary. Inclusion of concomitant genomic and proteomic-based molecular profiling techniques into clinical trial protocols will bring us closer to the reality of patient-tailored therapy.

An Interventional Magnetic Resonance Imaging Technique for the Molecular Characterization of Intraprostatic Dynamic Contrast Enhancement

The biological characterization of an individual patient's tumor by noninvasive imaging will have an important role in cancer care and clinical research if the molecular processes that underlie the image data are known. Spatial heterogeneity in the dynamics of magnetic resonance imaging contrast enhancement (DCE-MRI) is hypothesized to reflect variations in tumor angiogenesis. Here we demonstrate the feasibility of precisely colocalizing DCE-MRI data with the genomic and proteomic profiles of underlying biopsy tissue using a novel MRI-guided biopsy technique in a patients with prostate cancer.

Application of laser capture microdissection and protein microarray technologies in the molecular analysis of airway injury following pollution particle exposure

Understanding the mechanisms by which various types of air pollution particles (particulate matter, PM) mediate adverse health effects would provide biological plausibility to epidemiological associations of increased rates of morbidity and mortality. The majority of information regarding the means by which PM generates lung injury has been derived from in vitro studies. However, it is unclear as to what extent these mechanisms can be extrapolated to the in vivo situation. Current methods to assess mechanisms of PM-induced lung injury make it difficult to obtain site-specific, sensitive, and comprehensive determinations of cellular and molecular pathology associated with PM-induced injury. In the present study, the ability of laser capture microdissection (LCM) and protein microarray technologies were assessed to examine the effect of residual oil fly ash (ROFA) exposure on airway intracellular signaling pathways and transcription factor activation. Sprague-Dawley rats were intratracheally instilled with 0.5 mg/rat of ROFA. LCM was used to recover airway cells and protein extracts derived from the microdissected airways were analyzed by protein microarray. ROFA exposure increased p-ERK:ERK and p-I kappa B:I kappa B, suggesting changes in cell growth, transformation, and inflammation within the airway. These results are consistent with previously reported in vitro findings, demonstrating for the first time the credibility of applying LCM and protein microarray technologies to assess acute lung injury induced by environmental air pollutants.

Promising directions for the diagnosis and management of gynecological cancers

Diagnosis and management of cancer requires tools with both high sensitivity and specificity. The minimally invasive cervical smear has demonstrated how a test, even one with low specificity, can change the public health profile of a cancer from a late stage deadly disease to early diagnosis with rare tumor-related deaths. The benefit of such a test is best demonstrated by the low frequency of cervix cancer and its good outcome in countries where this test is readily available and used with appropriate secondary follow up. Early and specific symptoms, and identification and prevention for high risk groups has had similar impact for endometrial cancer. Neither a robust test, nor reliable or specific early symptoms are available for ovarian cancer, making clinical and scientific advances in this area a critical world-wide need. Current approaches testing one protein or gene marker at a time will not address this crisis expeditiously. New sensitive, specific, accurate, and reliable technologies that can be implemented using high throughput mechanisms are needed at as low a cost as possible. Ideally, these technologies should be focused on readily available patient resources, such as blood or urine, or as in the case of cervix cancer, minimally invasive informative approaches such as cervical smears. Techniques that allow data mining from a large input database overcome the slow advances of one protein-one gene investigation, and further address the multi-faceted carcinogenesis process occurring even in germ line mutation-associated malignancy. Proteomics, the study of the cellular proteins and their activation states, has led the progress in biomarker development for ovarian and other cancers and is being applied to management assessment. Amenable to high throughput, internet interface, and representative of the proteome spectrum, proteomic technology is the newest and most promising direction for translational developments in gynecologic cancers.

Proteomic approaches to the diagnosis, treatment, and monitoring of cancer

The field of proteomics holds promise for the discovery of new biomarkers for the early detection and diagnosis of disease, molecular targets for therapy and markers for therapeutic efficacy and toxicity. A variety of proteomics approaches may be used to address these goals. Two-dimensional gel electrophoresis (2D-PAGE) is the cornerstone of many discovery-based proteomics studies. Technologies such as laser capture microdissection (LCM) and highly sensitive MS methods are currently being used together to identify greater numbers of lower abundance proteins that are differentially expressed between defined cell populations. Newer technologies such as reverse phase protein arrays will enable the identification and profiling of target pathways in small biopsy specimens. Surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) analysis enables the high throughput characterization of lysates from very few tumor cells or body fluids and may be best suited for diagnosis and monitoring of disease. Such technologies are expected to supplement our arsenal of mRNA-based assays, and we believe that in the future, entire cellular networks and not just a single deregulated protein will be the target of therapeutics and that we will soon be able to monitor the status of these pathways in diseased cells before, during and after therapy.

Cancer diagnosis using proteomic patterns

The advent of proteomics has brought with it the hope of discovering novel biomarkers that can be used to diagnose diseases, predict susceptibility and monitor progression. Much of this effort has focused upon the mass spectral identification of the thousands of proteins that populate complex biosystems such as serum and tissues. A revolutionary approach in proteomic pattern analysis has emerged as an effective method for the early diagnosis of diseases such as ovarian cancer. Proteomic pattern analysis relies on the pattern of proteins observed and does not rely on the identification of a traceable biomarker. Hundreds of clinical samples per day can be analyzed utilizing this technology, which has the potential to be a novel, highly sensitive diagnostic tool for the early detection of cancer.

Site-directed mutations in the tumor-associated cytokine, autotaxin, eliminate nucleotide phosphodiesterase, lysophospholipase D, and motogenic activities

The exo-enzyme autotaxin/NPP2 (ATX/NPP2) is a potent stimulator of cell migration, invasion, metastasis, and angiogenesis. Recently, ATX/NPP2 was found to possess lysophospholipase D (lyso-LPD) activity, generating the bioactive mediator lysophosphatidic acid from precursors. In the present study, we used site-directed mutagenesis to delineate the active domain of lysophospholipid catalytic activity and to examine potential overlap with the nucleotide phosphodiesterase domain. We found four amino acid residues obligatory for the phosphodiesterase, lyso-PLD, and migration-stimulating activities of ATX/NPP2, suggesting that 5'-nucleotide phosphodiesterase (PDE) and lyso-PLD share a common reaction mechanism and inviting design of enzymatic inhibitors as therapeutic agents for neoplastic disease.

Time-resolved X-ray powder diffraction on a three-way catalyst at the GILDA beamline

Time-resolved X-ray diffraction experiments carried out at the beamline BM08-GILDA of ESRF allowed a study of the structural modifications taking place in a Pt/ceria-zirconia catalyst while the CO oxidation reaction was in progress. The capillary tube in which the sample is stored acts effectively as a chemical microreactor that ensures homogeneity of the sample treatments and minimization of diffusion effects. During the flowing of the reactant CO/He mixture, the investigated catalyst undergoes a fast Ce(IV)-Ce(III) partial reduction that involves the release of one O atom for every two reduced Ce cations. Because Ce(III) has a larger ionic radius than Ce(IV), the structural modification produces an increase of the lattice constant of the ceria-zirconia mixed oxide, and this increase is monitored by the translating imaging-plate device implemented at GILDA. The CO(2) resulting from the oxidation of the fluxed CO is monitored by a quadrupole mass spectrometer during the recording of the time-resolved X-ray diffraction pattern. The chemical and structural information was combined to show that the CO(2) yield is nearly constant until the catalytic system can provide oxygen for the reaction, while the structural rearrangement of the catalyst is delayed with respect to the switching on of the CO/He flux. After this induction time, during which CO(2) is produced with no structural modification of the catalyst, a fast increase of the lattice constant takes place.

Future research directions in idiopathic pulmonary fibrosis: summary of a National Heart, Lung, and Blood Institute working group

Idiopathic pulmonary fibrosis (IPF) is an insidious inflammatory fibroproliferative disease whose cause and course before diagnosis are unknown, and for which existing treatments are of limited benefit. The National Heart, Lung, and Blood Institute convened a working group to develop specific recommendations for future IPF research. Inflammatory and immune processes are involved in IPF pathogenesis, and current therapeutic strategies are aimed at suppressing the inflammation. Recent data suggest that the molecular processes underlying the fibrogenesis may provide new opportunities for therapeutic intervention. Specific areas of future research recommended by the working group include studies to elucidate the etiology of IPF, to develop novel diagnostic techniques and molecular diagnostics, to establish a program for identification of molecular targets for IPF treatment and identification and generation of agonists or antagonists that inhibit fibrogenesis, to foster investigations that couple the use of new technologies (e.g., laser capture microdissection, microarrays, and mass spectroscopic analysis of proteins) with data from the human genome project, to establish a national consortium of Clinical Centers of Excellence to conduct coordinated clinical and laboratory studies of well-characterized patients and patient-derived materials, and to stimulate research to develop animal models of persistent and progressive pulmonary fibrosis for evaluation of new intervention approaches.

Soluble adhesion molecules: marker of pre-eclampsia and intrauterine growth restriction

OBJECTIVE

This study monitored circulating plasma levels of soluble vascular cellular adhesion molecule-1 (sVCAM-1), intracellular adhesion molecule-1 (sICAM-1) and soluble E-selectin (sE-selectin) in women with healthy pregnancies, with pregnancy-induced hypertension (PIH), with pre-eclampsia and with pregnancies with isolated intrauterine growth restriction (IUGR) in order to determine whether elevated concentrations have a predictive value for the clinical signs of those pregnancy-induced disorders.

METHODS

Plasma concentrations of sVCAM-1, sICAM-1 and sE-selectin were determined in healthy pregnant women at each trimester of pregnancy and in pregnant women with PIH, pre-eclampsia and IUGR using commercial kits.

RESULTS

In the group of healthy pregnant women, plasma levels of sVCAM-1, sICAM-1 and sE-selectin did not change throughout pregnancy. No significant differences in the levels of these molecules were observed between healthy pregnant women at the third trimester of pregnancy and women with PIH. In addition, concentrations of soluble adhesion molecules were significantly higher in women with pre-eclampsia than in the group of women with healthy pregnancies. Only sVCAM-1 and sE-selectin levels were significantly higher in women with IUGR compared to healthy pregnant women.

CONCLUSIONS

Abnormally circulating levels of sVCAM-1, sICAM-1 and sE-selectin may have a predictive value for pre-eclampsia and IUGR, as they may be linked with endothelial activation and/or damage.

Recognition of multiple classes of hepatitis C antibodies increases detection sensitivity in oral fluid

Paired serum-oral fluid samples from 127 hepatitis C virus (HCV)-positive and 31 HCV-negative patients were tested for the presence of anti-HCV using the Ortho HCV 3.0 ELISA. Using the immunoglobulin G (IgG)-specific detection antibody provided with the HCV 3.0 ELISA we attained 100% sensitivity and specificity with serum samples; however, sensitivity in oral fluid samples was only 81%. By modifying the HCV 3.0 ELISA to utilize a secondary antibody cocktail that recognizes not only IgG but IgA and IgM as well, we attained 100% specificity and sensitivity with oral fluid samples.

Signal pathways which promote invasion and metastasis: critical and distinct contributions of extracellular signal-regulated kinase and Ral-specific guanine exchange factor pathways

Approximately 50% of metastatic tumors contain Ras mutations. Ras proteins can activate at least three downstream signaling cascades mediated by the Raf-MEK-extracellular signal-regulated kinase family, phosphatidylinositol-3 (PI3) kinase, and Ral-specific guanine nucleotide exchange factors (RalGEFs). Here we investigated the contribution of RalGEF and ERK activation to the development of experimental metastasis in vivo and associated invasive properties in vitro. Each pathway contributes distinct properties to the metastatic phenotype. Following lateral tail vein injection, 3T3 cells transformed by constitutively active Raf or MEK produced lung metastasis that displayed circumscribed, noninfiltrating borders. In contrast, 3T3 cells transformed by Ras(12V,37G), a Ras effector mutant that activates RalGEF but not Raf or P13 kinase, formed aggressive, infiltrative metastasis. Dominant negative RalB inhibited Ras(12V,37G)-activated invasion and metastasis, demonstrating the necessity of the RalGEF pathway for a fully transformed phenotype. Moreover, 3T3 cells constitutively expressing a membrane-associated form of RalGEF (RalGDS-CAAX) formed invasive tumors as well, demonstrating that activation of a RalGEF pathway is sufficient to initiate the invasive phenotype. Despite the fact that Ras(12V,37G) expression does not elevate ERK activity, inhibition of this kinase by a conditionally expressed ERK phosphatase demonstrated that ERK activity was necessary for Ras(12V,37G)-transformed cells to express matrix-degrading activity in vitro and tissue invasiveness in vivo. Therefore, these experiments have revealed a hitherto-unknown but essential interaction of the RalGEF and ERK pathways to produce a malignant phenotype. The generality of the role of the RalGEF pathway in metastasis is supported by the finding that Ras(12V,37G) increased the invasiveness of epithelial cells as well as fibroblasts.

Centrosome defects can account for cellular and genetic changes that characterize prostate cancer progression

Factors that determine the biological and clinical behavior of prostate cancer are largely unknown. Prostate tumor progression is characterized by changes in cellular architecture, glandular organization, and genomic composition. These features are reflected in the Gleason grade of the tumor and in the development of aneuploidy. Cellular architecture and genomic stability are controlled in part by centrosomes, organelles that organize microtubule arrays including mitotic spindles. Here we demonstrate that centrosomes are structurally and numerically abnormal in the majority of prostate carcinomas. Centrosome abnormalities increase with increasing Gleason grade and with increasing levels of genomic instability. Selective induction of centrosome abnormalities by elevating levels of the centrosome protein pericentrin in prostate epithelial cell lines reproduces many of the phenotypic characteristics of high-grade prostate carcinoma. Cells that transiently or permanently express pericentrin exhibit severe centrosome and spindle defects, cellular disorganization, genomic instability, and enhanced growth in soft agar. On the basis of these observations, we propose a model in which centrosome dysfunction contributes to the progressive loss of cellular and glandular architecture and increasing genomic instability that accompany prostate cancer progression, dissemination, and lethality.