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PubMed2000

Cytokeratin 7 and 20 expression in choroid plexus tumors: utility in differentiating these neoplasms from metastatic carcinomas.

Tumors derived from choroid plexus epithelium are uncommon and may exhibit a wide variety of histologic patterns. They often are difficult to distinguish from metastatic carcinomas. Previous studies that addressed this issue yielded conflicting results. Recent reports have demonstrated that evaluation of coordinate expression of cytokeratin (CK) 7 and CK20 aids in distinguishing primary from metastatic lesions in a number of anatomic sites and that tumors that commonly are metastatic to the brain retain their CK7/CK20 immunophenotype in this location. We examined 35 choroid plexus tumors with a panel of antibodies to determine their CK7/CK20 immunophenotype. Tumors from 35 patients (7 male, 28 female; mean age, 25 years), including 31 choroid plexus papillomas and 4 atypical papillomas, were evaluated. All tumors were intraventricular or within the cerebellopontine angle and composed predominantly of orderly columnar epithelial cells resting on distinct fibrovascular cores. Atypical papillomas contained combinations of focal loss of architectural pattern, increased mitotic activity, necrosis, and brain parenchymal invasion. No lesion was unequivocally malignant. Twenty-six tumors (74%), including all atypical papillomas, were CK7 positive and CK20 negative. Two tumors stained with both markers, one stained with CK20 only, and six stained with neither marker. Other findings included expression of glial fibrillary acidic protein in 24 tumors, S-100 protein in 19 tumors, transthyretin in 31 tumors, Ber EP4 in 1 tumor, CAM5.2 in 33 tumors, epithelial membrane antigen in 4 tumors, and pancytokeratin in 27 tumors. Our results indicate that the majority of choroid plexus tumors have a CK7-positive/CK20-negative immunophenotype. This finding may be useful in differentiating these lesions from metastatic carcinomas that have differing CK7/CK20 profiles.

Adolescent↗
PubMed2004

Noninvasive diagnosis of liver cirrhosis using DNA sequencer-based total serum protein glycomics.

We applied our 'clinical glycomics' technology, based on DNA sequencer/fragment analyzers, to generate profiles of serum protein N-glycans of liver disease patients. This technology yielded a biomarker that distinguished compensated cirrhotic from noncirrhotic chronic liver disease patients, with 79% sensitivity and 86% specificity (100% sensitivity and specificity for decompensated cirrhosis). In combination with the clinical chemistry-based Fibrotest biomarker, compensated cirrhosis was detected with 100% specificity and 75% sensitivity. The current 'gold standard' for liver cirrhosis detection is an invasive, costly, often painful liver biopsy. Consequently, the highly specific set of biomarkers presented could obviate biopsy in many cirrhosis patients. This biomarker combination could eventually be used in follow-up examinations of chronic liver disease patients, to yield a warning that cirrhosis has developed and that the risk of complications (such as hepatocellular carcinoma) has increased considerably. Our clinical glycomics technique can easily be implemented in existing molecular diagnostics laboratories.

Blood Proteins↗
PubMed2001

Diabetes mellitus a risk for osteoporosis?

Localized lesions at the foot skeleton are a serious and well recognized complication of diabetes mellitus which may impair the clinical outcome of the patients remarkably. In contrast, the presence of a generalized bone disease or osteoporosis related to diabetes mellitus is less acknowledged and its clinical relevance is less obvious. This paper is a clinically focused review of the literature on osteoporosis related to diabetes mellitus. Due to the different pathogenesis of diabetes mellitus type 1 and type 2 it is not surprising that there is no uniform entity of diabetic osteopathy. The majority of clinical studies in subjects with diabetes mellitus type 1 showed a moderately decreased bone mass at the forearm, while bone mass at the femur or lumbar spine was either decreased or not different from non-diabetic controls. In patients with diabetes mellitus type 2 the risk of osteopenia is not as clear as in type 1 diabetes. Bone mineral density at the forearm in patients with type 2 diabetes mellitus was decreased, unchanged or even increased in comparison to controls, while bone mineral density at the vertebrae or femoral neck was either not significantly different or increased, but rarely decreased. The underlying mechanisms triggering changes in bone mass in patients with diabetes mellitus type 1 and type 2 are not well known. In most studies there was no consistent relationship between the metabolic control of diabetes and bone mineral density. Biochemical parameters of the calcium and bone metabolism showed no clear relationship to the bone mineral density measurements. From few bone histology studies in humans and experimental studies there is evidence that a decreased bone formation is one major mechanism leading to reduced bone mass in diabetics. Microangiopathy at the bone tissue was also discussed as a possible reason for diabetic osteopenia. It was shown that insulin and insulin like growth factors (IGF-1, IGF-2) have an influence on bone metabolism itself and other growth factors, cytokines and hormones may determine changes in diabetic bone metabolism. Recent findings suggest that leptin is involved in the regulation of osteoblast function and bone mass, which is of special interest in diabetes mellitus type 2. The clinical relevance of osteoporosis or osteopenia is determined by the increased risk for insufficiency fractures. Few studies found an increased fracture risk, especially in older women with type 1 diabetes mellitus, while others did not show an increased risk for fractures or even found a decreased rate of fractures in women with diabetes mellitus type 2. There is a need for further longitudinal studies, including the incidence and risk factors for osteoporotic fractures. In clinical routine the extent of diagnostic and therapeutic activities in patients with type 1 or type 2 diabetes mellitus in respect to generalized bone disease or diabetic osteopenia should be based on individual conditions and risk profile for osteoporosis.

Animals↗
PubMed2006

Gene expression profiling in lung tissues from mice exposed to cigarette smoke, lipopolysaccharide, or smoke plus lipopolysaccharide by inhalation.

The purpose of this study was to investigate whether coexposure to lipopolysacchride (LPS) will heighten the inflammatory response and other pulmonary lesions in mice exposed to cigarette smoke, and thus to evaluate the potential use of this LPS-compromised mouse model as a model for chronic obstructive pulmonary disease (COPD) investigation. AKR/J male mice were exposed to HEPA-filtered air (sham control group), cigarette smoke (smoke group), LPS (LPS group), or smoke plus LPS (smoke-LPS group) by nose-only inhalation. Lungs were collected at the end of the 3-wk exposure and processed for microarray analysis. Clustering and network analysis showed decreased heat-shock response and chaperone activity, increased immune and inflammatory response, and increased mitosis in all three exposed groups. Two networks/function modules were exclusively found in the smoke-LPS group, that is, the downregulated muscle development/muscle contraction process and the upregulated reactive oxygen species production process. Notably, the number of genes and function modules/networks associated with inflammation was reduced in the smoke-LPS group compared to the LPS group. The most upregulated gene in the smoke group, MMP12, is a matrix metalloproteinase that preferentially degrades elastin and has been implicated in COPD development. NOXO1, which was upregulated in all three treatment groups, positively regulates the expression of a subunit of NADPH oxidase (NOX1), a major source of reactive oxygen species, and may play an important role in the pathogenesis of COPD. Serum amyloid A1, which is an acute-phase systemic inflammation marker and can be induced by LPS exposure, was significantly upregulated in the LPS and smoke-LPS groups. MARCO, a scavenger receptor expressed in macrophages that may play a significant role in LPS-induced inflammatory response, was upregulated in the LPS group and the smoke-LPS group, but not in the smoke group. In conclusion, gene expression profiling identified genes and function modules that may be related to COPD pathogenesis and may be useful as biomarkers to monitor COPD progression. In addition, an LPS-compromised mouse model showed potential as a useful tool for studying cigarette smoke-associated COPD.

Administration, Inhalation↗
PubMed2004

Proteomics in nephrology: current status and future directions.

Proteomics is one among various 'OMICS' fields that have been growing rapidly in the postgenomic era. During the past few years, proteomics has been extensively applied to several fields of medicine to better understand normal physiology, to define the pathophysiology of diseases, and to identify novel biomarkers and new therapeutic targets. This review focuses on current status and future directions of proteomics in the nephrology field. Recent studies of renal proteome, proteomes of individual intrarenal structures (i.e., glomerular, vascular, tubular, brush border membrane, mesangial, and podocyte proteomes), urinary proteome, and protein profiles in dialysate or ultrafiltrate removed by renal replacement therapy are summarized.

Animals↗
PubMed2002

A study on human urine in a high-selenium area of China by 1H-NMR spectroscopy.

In this study, high-resolution 600-MHz 1H-NMR (nuclear magnetic resonance) spectroscopies were used to compare the urinary metabolic profiles of healthy humans and humans in a high-selenium area of China. NMR biomarkers for renal and liver lesions were observed by comparing the urine 1H-NMR spectra. In urinary excretion, the concentrations in human urine samples of formate, lactate, acetate, hippurate, and alanine in overexposure to selenium were increased, whereas citrate, creatine, and TMAO excretion were decreased compared with that of the healthy human--some of them even disappeared. An interesting result was the appearance of formate in urine, which has previously been shown to lead to acidosis and chronic renal failure and interfere with the lumen and proximal tubular cells. The level of creatine was associated with the seminal activity. The changes of acetate and citrate may explain the disorder of the cellular energy metabolism caused by selenium, and the changes of other amino acids were a result of the reuptake of these compounds that had been blocked in the glomerulus and proximal tubule. The results elucidate the renal/liver lesion in humans in high-selenium area by 1H-NMR spectroscopy and offer the molecular basic of selenium toxicity.

China↗
PubMed2005

Have we made progress in pharmacogenomics? The implementation of molecular markers in colon cancer.

For the last 40 years, 5-fluorouracil (5-FU) has remained the treatment of choice in both the adjuvant and advanced treatment of colorectal cancer (CRC). However, 5-FU monotherapy produces response rates of only 10-20% in the advanced setting. 5-FU has been combined with newer agents, such as oxaliplatin and irinotecan, and this has significantly increased response rates to 40-50% in the advanced setting. More recently, novel biological agents, such as the monoclonal antibodies targeting either the epidermal growth factor receptor or vascular endothelial growth factor, have shown to provide additional clinical benefit for patients with metastatic CRC. A number of predictive markers have been identified for CRC to date. However, their usefulness as individual markers of response has led to somewhat inconclusive results. Therefore, there is a need to identify panels of predictive markers of response to therapy for advanced CRC, in order to improve these disappointing response rates. The advent of high-throughput methodologies, such as microarrays, enables tumor samples to be profiled on a global scale. This technology has been utilized to develop predictive markers for a wide range of tumor types to date, and hopefully this technology can be translated into the CRC setting with the hope of predicting the response of each individual tumor to chemotherapy.

Antibodies, Monoclonal↗
PubMed1992

[Proteins associated with nucleolar organizer regions: practical application in tumor histopathology and relationship to biological properties of the tumor].

The argyrophilic staining of nucleolar organizer regions (AgNOR) has been found to be of increasing use in routine and experimental histopathology in the study of certain neoplastic lesions. The AgNOR reaction demonstrates the presence of argyrophilic non-histone proteins within NORs. The number of detectable NORs depends on several factors: the level of transcriptional activity, the number of NOR-bearing chromosomes in the karyotype, and the stage of the cell cycle in which they are sought. In man, five chromosomes have NORs, and these areas are the sites which hybridize with rRNA and are of importance with respect to the ultimate synthesis of protein. The results of AgNORs might be more informative if this technique would be applied simultaneously in cytological and histological specimens for each patient. It may also be important to examine the AgNORs profiles in stromal cells.

Biomarkers, Tumor↗
PubMed1989

Postoperative changes in lipid profile: their relations with inflammatory markers and endocrine mediators.

Postoperative changes in plasma lipid profile have been studied in six patients undergoing aortobifemoral bypass. The second day after surgery, significant changes were: decreased levels of high density lipoprotein (HDL) cholesterol (by 55%), non HDL cholesterol (by 60%) phospholipid (by 50%), pre-beta-lipoprotein (by 70%), beta-lipoprotein (by 50%), apolipoprotein A1 (by 60%) and apolipoprotein B (by 55%). The magnitude of these changes correlated positively with serum levels of transferrin and negatively with serum levels of C-reactive protein. Triglyceride levels also showed a significant decrease (by 60%) while free fatty acids increased by 70%. Changes in triglyceride levels were not correlated with serum transferrin and C-reactive protein but showed a significant negative correlation with insulin levels. Our results suggest that both inflammatory and endocrine mediators are likely implicated in the postoperative changes in lipid profile.

Biomarkers↗
PubMed2026

Proteomic Profile Differences in Immune-Related Diseases in Pediatric Patients Under Five Years Old: Asthma and IgE-Dependent Allergies-A Pilot Study.

Asthma is a heterogeneous disease that often begins in childhood and frequently occurs alongside allergic conditions. In asthma research, it is important to focus on proteins that are the primary regulators of cellular physiology. The differences in the proteome between children with asthma and those with an atopic background remain poorly understood. The present study included 130 serum samples from four groups of pediatric patients under the age of five: (1) with asthma and IgE-dependent allergies; (2) with non-atopic asthma; (3) non-asthmatics with IgE-dependent allergy; and (4) a control group without asthma and IgE-dependent allergies. The serum samples were used for protein-peptide profiling and proteomic identification using nanoLC-MALDI-TOF/TOF MS/MS. The obtained data were analyzed using univariate statistics and the STRING tool v12.0 to identify protein-protein potential interactions. A total of seven proteins were identified as discriminative between the study groups: A2M, AACT, IgG3, C3, ITIH2, IgG3 and IGK. All of them were upregulated in patients with IgE-dependent allergy compared to other study groups. STRING analysis identified functional associations among four proteins (AACT, A2M, C3, and ITIH2) with discriminatory potential for distinguishing between non-atopic asthma and non-asthmatic patients with IgE-dependent allergy. The results suggest that the identified putative protein markers overlap in cellular pathways, including those associated with the pathophysiology of asthma and allergic disorders. These findings provide further insight into the overall proteomic profile of pediatric patients with asthma and IgE-dependent allergy, highlighting its heterogeneity across the analyzed groups.

Humans↗
PubMed2005

Iterative microarray and RNA interference-based interrogation of the SRC-induced invasive phenotype.

Src kinase has long been recognized as a factor in the progression of colorectal cancer and seems to play a specific role in the development of the metastatic phenotype. In spite of numerous studies conducted to elucidate the exact role of Src in cancer progression, downstream targets of Src remain poorly understood. Gene expression profiling has permitted the identification of large sets of genes that may be functionally interrelated but it is often unclear as to which molecular pathways they belong. Here we have developed an iterative approach to experimentally reconstruct a network of gene activity regulated by Src and contributing to the invasive phenotype. Our strategy uses a combination of phenotypic anchoring of gene expression profiles and loss-of-function screening by way of RNA-mediated interference. Using a panel of human colon cancer cell lines exhibiting differential Src-specific activity and invasivity, we identify the first two levels of gene transcription responsible for the invasive phenotype, where first-tier genes are controlled by Src activity and the second-tier genes are under the influence of the first tier. Specifically, perturbation of first-tier gene activity by either pharmacologic inhibition of Src or RNA-mediated interference-directed knockdown leads to a loss of invasivity and decline of second-tier gene activity. The targeting of first-tier genes may be bypassed altogether because knockdown of second-tier genes led to a similar loss of invasive potential. In this manner, numerous members of a "transcriptional cascade" pathway for metastatic activity have been identified and functionally validated.

Biomarkers, Tumor↗
PubMed2002

The polycomb group protein EZH2 is involved in progression of prostate cancer.

Prostate cancer is a leading cause of cancer-related death in males and is second only to lung cancer. Although effective surgical and radiation treatments exist for clinically localized prostate cancer, metastatic prostate cancer remains essentially incurable. Here we show, through gene expression profiling, that the polycomb group protein enhancer of zeste homolog 2 (EZH2) is overexpressed in hormone-refractory, metastatic prostate cancer. Small interfering RNA (siRNA) duplexes targeted against EZH2 reduce the amounts of EZH2 protein present in prostate cells and also inhibit cell proliferation in vitro. Ectopic expression of EZH2 in prostate cells induces transcriptional repression of a specific cohort of genes. Gene silencing mediated by EZH2 requires the SET domain and is attenuated by inhibiting histone deacetylase activity. Amounts of both EZH2 messenger RNA and EZH2 protein are increased in metastatic prostate cancer; in addition, clinically localized prostate cancers that express higher concentrations of EZH2 show a poorer prognosis. Thus, dysregulated expression of EZH2 may be involved in the progression of prostate cancer, as well as being a marker that distinguishes indolent prostate cancer from those at risk of lethal progression.

Biomarkers, Tumor↗
PubMed2003

Cancer target discovery using SAGE.

Cancer is a genetic disease. Genetic events including mutations, chromosomal gains, losses and rearrangements, along with epigenetic alterations, lead to significant transcriptional changes in cancer cells. Changes in the expression of many genes associated with the onset and progression of cancer likely contribute to the cancerous phenotype. SAGE (Serial Analysis of Gene Expression) is an expression profiling method that allows for global, unbiased and quantitative characterisation of transcriptomes. The expression of thousands of genes can be analysed simultaneously without prior knowledge of their sequence, thus leading to the discovery of novel transcripts. In addition to characterising normal and malignant gene expression patterns, SAGE can be used to identify downstream targets of tumour suppressors and oncogenes and further annotate genomes. Comprehensive analyses of expression profiles using SAGE will yield many new diagnostic and prognostic markers as well as therapeutic targets in cancer.

Antineoplastic Agents↗
PubMed2004

Surface-enhanced laser desorption/ionization-time of flight-mass spectrometry approach to biomarker discovery in blue mussels (Mytilus edulis) exposed to polyaromatic hydrocarbons and heavy metals under field conditions.

Proteomics provide potential in the discovery of new sensitive biomarkers for environmental pollution. To evaluate this potential, we have utilized ProteinChip technology to analyze the proteomic profile of blue mussels (Mytilus edulis) from polluted marine habitats surrounding the island of Karmøy, Norway. Two different types of contamination, heavy metals and polyaromatic hydrocarbons (PAHs), were compared to a clean reference site. Differentially expressed proteins/peptides were found, which showed a specific induction or a general suppression associated with the field site of origin. By combining sets of protein markers in a tree-building algorithm, we were able to correctly classify samples from these sites with an accuracy of 90%.

Algorithms↗
PubMed2003

Malignant fibrous histiocytoma: a proposed cellular origin and identification of its characterizing gene transcripts.

Although malignant fibrous histiocytoma (MFH) is one of the most diffuse and highly aggressive tumors among soft tissue sarcomas in adults, it is poorly characterized from the molecular point of view. The overt lack of expression of phenotypic markers in MFH cells and the hypothesis that MFH may originate from transformed multipotent stem/progenitor cells with mesenchymal features has led us to investigate this notion and search for 'MFH-specific' genes. To address this problem, we have undertaken a differential display-based three-pair comparative mRNA profiling of bone-marrow derived mesenchymal stem cells (MSC) and cells isolated by primary MFH, leiomyosarcoma and smooth muscle cells, fibrosarcoma and dermal fibroblasts. This approach highlighted pair-wise analogies in gene expression patterns between matched tumor and healthy cells and yielded direct access to 43 genes differentially expressed between MSC and MFH cells. Eleven of the identified genes were selected for comparative evaluation of their expression levels in other sarcoma types, as well as potential markers for the detection of circulating tumor cells. Several of these genes defined the stem/progenitor versus MFH cell and some of them have the potential to be exploited for disclosure of circulating sarcoma cells. The striking similarity in the gene expression patterns observed in the two cell types was further corroborated by a remarkable similarity in the cell phenotypic markers that these cells expressed ex vivo. The findings open now the possibility to examine, also functionally, genes not previously known to be implicated in MFH development and strengthen the hypothesis that MFH originates from a mesenchymal progenitor cell.

Biomarkers, Tumor↗
PubMed2006

Integrated breast cancer genomics.

Predicting survival and therapy responses of breast cancer patients is a significant challenge. Two studies in this issue of Cancer Cell present a novel integrated analysis of genomic and transcriptomic profiles of 145 primary breast cancers and 51 established cell lines. Data from clinical tumors highlighted mechanisms of disease and facilitated identification of potential therapeutic targets and prognostic biomarkers. An extensive well-characterized cancer cell line resource opens up opportunities to explore the determinants of cellular responses to existing and emerging therapies. Taken together, these studies illustrate how integrated molecular profiling may one day significantly impact diagnosis and therapeutic choice in human breast cancer.

Breast Neoplasms↗
PubMed2005

Molecular typing of adult acute myeloid leukaemia: significance of translocations, tandem duplications, methylation, and selective gene expression profiling.

Although a number of molecular aberrations have been described in acute myeloid leukaemia (AML), no study has yet determined their relative prognostic importance. We have analysed blast cells from 250 adult patients treated at the same institution during a 15-year period. Balanced translocations were detected by multiplex polymerase chain reaction in 13% of the cases. Internal tandem duplication (ITD) of the FLT3 gene and partial tandem duplication of the MLL gene were found in 24% and 4%, respectively. Promoter hypermethylation of the P15, CDH1, ER and MDR1 genes was observed in 71%, 64%, 40% and 4%, respectively. Compared with normal bone marrow, the chemotherapy resistance protein MRP1 and apoptosis related genes BAX and CASPASE3 were found to be overexpressed in AML blasts. Univariate analysis revealed that the most important determinants of prognosis were presence of balanced translocations, age, white blood cell count and extramedullary disease, in order of statistical significance. In a multivariate analysis, balanced translocations retained their prognostic significance and FLT3 ITD as well as high gene expression of MDR1 were negative prognostic factors. From these data, which are the first to compare these molecular aberrations directly, we conclude that, when a battery of molecular changes is evaluated for upfront significance in AML, recurrent translocations are of prime importance for treatment outcome.

Acute Disease↗
PubMed2003

New algorithms for multi-class cancer diagnosis using tumor gene expression signatures.

MOTIVATION: The increasing use of DNA microarray-based tumor gene expression profiles for cancer diagnosis requires mathematical methods with high accuracy for solving clustering, feature selection and classification problems of gene expression data. RESULTS: New algorithms are developed for solving clustering, feature selection and classification problems of gene expression data. The clustering algorithm is based on optimization techniques and allows the calculation of clusters step-by-step. This approach allows us to find as many clusters as a data set contains with respect to some tolerance. Feature selection is crucial for a gene expression database. Our feature selection algorithm is based on calculating overlaps of different genes. The database used, contains over 16 000 genes and this number is considerably reduced by feature selection. We propose a classification algorithm where each tissue sample is considered as the center of a cluster which is a ball. The results of numerical experiments confirm that the classification algorithm in combination with the feature selection algorithm perform slightly better than the published results for multi-class classifiers based on support vector machines for this data set. AVAILABILITY: Available on request from the authors.

Algorithms↗