Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Biomarker Profiling”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 955 records · Page 53Linked to original sources
PubMed2005

Identification of cell surface marker candidates on SV-T2 cells using DNA microarray on DLC-coated glass.

We analyzed gene expression profiles of normal mouse fibroblast BALB/c 3T3 cells and its SV40 transformant SV-T2 cells using our originally developed cell surface marker DNA microarray, which is prepared on a diamond-like carbon-coated glass. As a result, CD62L and IL-6 receptor alpha gene expressions were upregulated in SV-T2 and were thought to be candidates for call surface markers of the cells. The result of microarray analysis was validated by real-time quantitative PCR immunohistochemistry and biological assays. These data show that our cell surface marker DNA microarray should be useful in finding the candidates of cell type-specific surface markers.

Animals↗
PubMed2004

Potential involvement of rainbow trout thrombocytes in immune functions: a study using a panel of monoclonal antibodies and RT-PCR.

The functional relationship between fish and mammalian thrombocytes is relatively unknown. In this study, a panel of monoclonal antibodies (mAbs) was used to investigate the functional properties of rainbow trout thrombocytes. The mAbs recognize cell-surface molecules on thrombocytes with molecular weights ranging from 17 to 160 kDa. Flow cytometric and immuno-electron microscopic analyses demonstrate that these molecules are expressed at different levels and that surface expression increased upon activation with bovine collagen. Two of these cell-surface molecules (17 and 21 kDa) were directly involved in collagen-induced aggregation of thrombocytes since aggregation was blocked upon pre-treatment with mAbs that recognize the two surface markers. Interestingly, the percentage of thrombocytes in blood increased after stimulation using different antigens. The transcriptional profile of trout thrombocytes was then examined after immuno-magnetic enrichment using the described mAbs to assess potential roles of trout thrombocytes in immune functions. Trout thrombocytes express components of the MHC class Ia pathway, IL1beta, TNFalpha, TGFbeta, the interleukin receptor common gamma chain as well as CXC and CC chemokines. MHC class IIB and TNFalpha were expressed at low levels in resting thrombocytes. No evidence was found for the expression of TCRalphabeta, Ig heavy chain, CD8alpha or CK1 mRNA. Taken together, these results suggest that rainbow trout thrombocytes express molecules involved in activation, aggregation and genes encoding proteins, that are involved in antigen presentation and immune regulation.

Animals↗
PubMed2005

Expressed genome molecular signatures of heart failure.

Traditional gene expression studies typically focus on one or a few genes of interest. An important limitation of single-gene studies is that they present a portrait of disease that is essentially static. However, disease is a dynamic process, driven by a combination of genetic, epigenetic and environmental factors. Recently, genomic technologies have permitted better characterization of the dynamic aspect of disease progression. Genome-wide expression profiles of cardiovascular diseases, heart failure in particular, using microarrays have been published and are providing new insights into this complex disease. Tissue biopsies required for traditional microarray studies, however, are often invasive and not readily available. By contrast, blood samples are relatively non-invasive and are readily available. In a number of recent studies, blood cells appear to be a viable substitute for tissue biopsy. Blood cells have the ability to mirror the body's tissues and organs in health and disease; thus, we hypothesize that blood cells can indicate at the molecular level the presence of disease. Here we review microarray gene expression profiling of blood RNA for a number of different diseases. Sieving through gene expression molecular signatures has identified groups of genes characteristic of each and has identified biomarkers associated with specific diseases.

Expressed Sequence Tags↗
PubMed2007

A specific gene-expression signature quantifies the degree of hepatic fibrosis in patients with chronic liver disease.

AIM: To study a more accurate quantification of hepatic fibrosis which would provide clinically useful information for monitoring the progression of chronic liver disease. METHODS: Using a cDNA microarray containing over 22000 clones, we analyzed the gene-expression profiles of non-cancerous liver in 74 patients who underwent hepatic resection. We calculated the ratio of azan-stained: total area, and determined the morphologic fibrosis index (MFI), as a mean of 9 section-images. We used the MFI as a reference standard to evaluate our method for assessing liver fibrosis. RESULTS: We identified 39 genes that collectively showed a good correlation (r > 0.50) between gene-expression and the severity of liver fibrosis. Many of the identified genes were involved in immune responses and cell signaling. To quantify the extent of liver fibrosis, we developed a new genetic fibrosis index (GFI) based on gene-expression profiling of 4 clones using a linear support vector regression analysis. This technique, based on a supervised learning analysis, correctly quantified the various degrees of fibrosis in both 74 training samples (r = 0.76, 2.2% vs 2.8%, P < 0.0001) and 12 independent additional test samples (r = 0.75, 9.8% vs 8.6%, P < 0.005). It was far better in assessing liver fibrosis than blood markers such as prothrombin time (r = -0.53), type IV collagen 7s (r = 0.48), hyaluronic acid (r = 0.41), and aspartate aminotransferase to platelets ratio index (APRI) (r = 0.38). CONCLUSION: Our cDNA microarray-based strategy may help clinicians to precisely and objectively monitor the severity of liver fibrosis.

Biomarkers↗
PubMed2005

Using proteomic approaches to identify new biomarkers for detection and monitoring of ovarian cancer.

OBJECTIVES: Early detection and monitoring the treatment remain the most important factors in improving long-term survival of ovarian cancer patients. New biomarkers that individually or in combination improve the diagnostic performance of existing tumor markers are critically needed. This study uses proteomic approaches to identify new biomarkers for detection and monitoring of ovarian cancer. METHODS: We analyzed protein profiles of three sets of sera using surface enhanced laser desorption and ionization time-of-light mass spectroscopy (SELDI-TOF-MS) on IMAC ProteinChip arrays and ProPeak software for bioinformatics data analysis. The first set of patients included 21 ovarian cancers, 18 benign diseases, and 20 normal patients. The second set included 32 ovarian cancers, 30 benign ovarian diseases, and 30 age-matched healthy controls. The third set included samples collected before and after chemotherapy from 18 ovarian cancer patients. All samples were collected at the Gynecology and Obstetrics Hospital of Fudan University in Shanghai, China. The datasets from low-intensity and high-intensity spectra were analyzed separately. RESULTS: Seven peaks were selected for their contribution to the separation of ovarian cancers from controls using the first and second set of samples. The same dysregulation trends were confirmed for six of the seven peaks in independent validation using the third set of samples. CONCLUSIONS: Using SELDI-TOF analysis of 195 unique specimens, we discovered with preliminary validation six distinct peaks that may potentially be useful in the detection and monitoring of ovarian cancer. Additional studies are required to determine the protein identities of these peaks and to further validate their performance as biomarkers.

Adult↗
PubMed2006

Microarray analysis of variation in individual aging C. elegans: approaches and challenges.

Aging is generally defined and studied as a population phenomenon. However, there is great interest, especially when discussing human aging, in the identification of factors that influence the life span of an individual organism. The nematode Caenorhabditis elegans provides an excellent model system for the study of aging at the level of the individual, since young nematodes are essentially clonal yet experience a large range of individual life spans. We are conducting gene expression profiling of individual nematodes, with the aim of discovering genes that vary stochastically in expression between individuals of the same age. Such genes are candidates to modulate the ultimate life span achieved by each individual. We here present statistical analysis of gene expression profiles of individual nematodes from two different microarray platforms, examining the issue of technical vs. biological variance as it pertains to uncovering genes of interest in this paradigm of individual aging.

Aging↗
PubMed2004

Discriminating different classes of toxicants by transcript profiling.

Male rats were treated with various model compounds or the appropriate vehicle controls. Most substances were either well-known hepatotoxicants or showed hepatotoxicity during preclinical testing. The aim of the present study was to determine if biological samples from rats treated with various compounds can be classified based on gene expression profiles. In addition to gene expression analysis using microarrays, a complete serum chemistry profile and liver and kidney histopathology were performed. We analyzed hepatic gene expression profiles using a supervised learning method (support vector machines; SVMs) to generate classification rules and combined this with recursive feature elimination to improve classification performance and to identify a compact subset of probe sets with potential use as biomarkers. Two different SVM algorithms were tested, and the models obtained were validated with a compound-based external cross-validation approach. Our predictive models were able to discriminate between hepatotoxic and nonhepatotoxic compounds. Furthermore, they predicted the correct class of hepatotoxicant in most cases. We provide an example showing that a predictive model built on transcript profiles from one rat strain can successfully classify profiles from another rat strain. In addition, we demonstrate that the predictive models identify nonresponders and are able to discriminate between gene changes related to pharmacology and toxicity. This work confirms the hypothesis that compound classification based on gene expression data is feasible.

Algorithms↗
PubMed2005

CD38 expression levels in chronic lymphocytic leukemia B cells are associated with activation marker expression and differential responses to interferon stimulation.

CD38, a surface protein whose expression increases upon normal B-cell activation, is a marker of disease aggression in B-cell chronic lymphocytic leukemia (B-CLL). Higher percentages of CD38-expressing CLL B cells may be found in lymphoid compartments compared to peripheral blood. Therefore, it is possible that although CLL B cells are resting, CD38 may be a marker of recent cell activation prior to entry into the periphery. To address this hypothesis, we examined the association of CD38 expression with other activation antigens identified in gene expression profiling experiments and include CD18, CD49d, CD20, and subunit 5 of the anaphase-promoting complex/cyclosome. We found that all these markers were more highly expressed in leukemic B cells from CD38-positive CLL patients. Lastly, because interferon is known to modulate CD38 expression, we used IFN-alpha to test the ability of CLL B cells to increase CD38 expression in vitro. Interestingly, IFN stimulation only modulated CD38 expression in CLL B cells that already expressed CD38. Taken together, these data suggest that CD38 is a marker of a more recently activated CLL B cell. This in turn may explain the biological and clinical differences between CD38-positive type B-CLL and CD38-negative type B-CLL.

ADP-ribosyl Cyclase 1↗
PubMed2004

The use of proteomics for the assessment of clinical samples in research.

Proteomics, the analysis of expressed proteins, has been an important developing area of research for the past two decades [Anderson, NG, Anderson, NL. Twenty years of two-dimensional electrophoresis: past, present and future. Electrophoresis 1996;17:443-453]. Advances in technology have led to a rapid increase in applications to a wide range of samples; from initial experiments using cell lines, more complex tissues and biological fluids are now being assessed to establish changes in protein expression. A primary aim of clinical proteomics is the identification of biomarkers for diagnosis and therapeutic intervention of disease, by comparing the proteomic profiles of control and disease, and differing physiological states. This expansion into clinical samples has not been without difficulties owing to the complexity and dynamic range in plasma and human tissues including tissue biopsies. The most widely used techniques for analysis of clinical samples are surface-enhanced laser desorption/ionisation mass spectrometry (SELDI-MS) and 2-dimensional gel electrophoresis (2-DE) coupled to matrix-assisted laser desorption ionisation [Person, MD, Monks, TJ, Lau, SS. An integrated approach to identifying chemically induced posttranslational modifications using comparative MALDI-MS and targeted HPLC-ESI-MS/MS. Chem. Res. Toxicol. 2003;16:598-608]-mass spectroscopy (MALDI-MS). This review aims to summarise the findings of studies that have used proteomic research methods to analyse samples from clinical studies and to assess the impact that proteomic techniques have had in assessing clinical samples.

Biomarkers↗
PubMed2004

[Screening of molecular markers of lung squamous cell carcinoma by microarrays].

OBJECTIVE: To identify molecular markers of lung squamous cell carcinoma by cDNA microarray technique. METHODS: cDNA expression profiles were examined by microarrays of 6 surgical specimens of stage I lung squamous cell carcinomas. Those genes, either up-regulated or down-regulated in every specimen studied, were identified. The expression levels of nm23 and BRCA2 by the squamous cell carcinoma of the lung were further examined by immunohistochemical techniques. RESULTS: A total of 107 genes were identified, of which 26 were up-regulated and 81 were down-regulated in all six specimens. Immunohistochemical staining showed that, compared with normal lung tissues, the intensity of nm23 expression by the squamous cell carcinoma of lung was significantly increased while that of BRCA-2 was decreased. CONCLUSION: cDNA microarrays can be used to identify gene expression profile of lung cancer, some of which may be used as markers of lung squamous cell carcinoma.

BRCA2 Protein↗
PubMed2004

ApcMin/+ mouse model of colon cancer: gene expression profiling in tumors.

The Apc(Min/+) mouse is a popular animal model for studies of human colon cancer, but the molecular changes associated with neoplasia in this system have only been partially characterized. Our aim was to identify novel genes involved in tumorigenesis in this model. RNA from intestinal adenomas and from pre-neoplastic small intestine were prepared from six Apc(Min/+) mice. The tumor transcriptomes were analyzed with high-density oligonucleotide microarrays representing approximately 12,000 probe sets; we compared their profiles with those of matched pre-neoplastic intestine. Stringent analysis revealed reproducible changes for 98 probe sets representing 90 genes, including novel observations regarding 50 genes whose involvement in this mouse model has never been reported. In addition to the expected changes in growth regulatory genes, the altered gene products could be assigned to four functional groupings that should enhance tumorigenesis: metabolic changes that would result in a high rate of glycolysis, alterations in enzymes involved in reactive oxygen species or carcinogen metabolism, cytoskeletal elements, and proteins involved in tumor invasion or angiogenesis. A fifth group consisted of expression changes that might restrict tumor progression, suggesting that the adenomatous state reflects a balance of pro- and anti-tumorigenic factors. Since many of the altered genes had not previously been reported to be involved in any tumorigenic processes, our observations provide a host of new candidates for potential modulation to prevent or treat intestinal neoplasia.

Adenomatous Polyposis Coli Protein↗
PubMed2003

Compensation for dystrophin-deficiency: ADAM12 overexpression in skeletal muscle results in increased alpha 7 integrin, utrophin and associated glycoproteins.

Mouse models for genetic diseases are among the most powerful tools available for developing and testing new treatment strategies. ADAM12 is a disintegrin and metalloprotease, previously demonstrated to significantly alleviate the pathology of mdx mice, a model for Duchenne muscular dystrophy in humans. More specifically ADAM12 appeared to prevent muscle cell necrosis in the mdx mice as evidenced by morphological analysis and by the reduced levels of serum creatine kinase. In the present study we demonstrated that ADAM12 may compensate for the dystrophin deficiency in mdx mice by increasing the expression and redistribution of several components of the muscle cell-adhesion complexes. First, we analyzed transgenic mice that overexpress ADAM12 and found mild myopathic changes and accelerated regeneration following acute injury. We then analyzed changes in gene-expression profiles in mdx/ADAM12 transgenic mice compared with their littermate controls and found only a few genes with an expression change greater than 2-fold between mdx/ADAM12 and mdx. The small changes in gene expression were unexpected, considering the marked improvement of the mdx pathology when ADAM12 is overexpressed, and suggested that significant changes in mdx/ADAM12 muscle might occur post-transcriptionally. Indeed, by immunostaining and immunoblotting we found an approximately 2-fold increase in expression, and distinct extrasynaptic localization, of alpha 7B integrin and utrophin, the functional homolog of dystrophin. The expression of the dystrophin-associated glycoproteins was also increased. In conclusion, these results demonstrate a novel way to alleviate dystrophin deficiency in mice, and may stimulate the development of new approaches to compensate for dystrophin deficiency in animals and humans.

ADAM Proteins↗
PubMed2005

Simultaneous measurement of gene expression for hepatotoxicity in thioacetamide-administered rats by DNA microarrays.

DNA microarray technology was developed as a tool for simultaneously measuring a number of gene expression changes, and has been applied for investigations of toxicity assessments of chemicals. In this study, we used a typical hepatotoxicant, thioacetamide (TA), to find correlations between the extent of hepatotoxicity and certain gene expression patterns or specific gene expression profiles. TA was intraperitoneally administered at high (400 mg/kg), medium (150 mg/kg) or low (50 mg/kg) dose (four rats per group) and then the serum and liver were collected at the indicated time (6, 12, 24, 36 and 48 h). Serum biochemical markers were measured and hepatic mRNA expression profiles were analyzed by a DNA microarray. Serum aspartate aminotransferase (AST) and alanine aminotransferase (ALT) were increased by TA-administration in a dose-dependent manner and reached the maximum at 24h. Hierarchical clustering analysis of all dosage groups revealed in 2 major clusters, distinguished by an early (6 and 12h) and a late (24, 36 and 48 h) phase. The early and late phase clusters were sorted in time- and dose-dependent manners. The major gene expression profile obtained by quality-threshold (QT) clustering analysis showed the same maximal toxic time as that estimated by the serum biochemical markers. The individual expression profiles of the candidate genes selected in our previous studies and the simultaneous gene expression patterns measured by five typical hepatotoxicants including TA also reflected the hepatotoxicity of TA. These findings suggest that the potential toxic effects appearing as gene expression changes are independent of the dosage of TA. This study suggested that the major gene expression profile estimated by QT clustering would be a sensitive marker of hepatotoxicity.

Alanine Transaminase↗
PubMed2005

Specific gene expression patterns in liver cirrhosis.

Liver cirrhosis (LC) is a complex disease that can develop into hepatocellular carcinoma (HCC). In an effort to investigate genetic differences between LC and HCC, we used cDNA microarray analysis to characterize the gene expression profiles in LC and HCC tissues. Consistent differences were observed among the expression patterns in LC, HCC, and normal liver tissues. Interestingly, the expression patterns of LC without tumor association (LCT) were also readily distinguished from those of LC tissues near hepatic tumor tissues (near-tumor tissue, NTT). Moreover, 25 cirrhosis-specific genes could be used to divide the NTT samples into two groups: inflammatory active cirrhosis (NTTa) and inflammatory inactive cirrhosis (NTTi). We found that NTTa samples showed gene expression patterns similar to those of the LCT and HCC groups, whereas the expression patterns of the NTTi group were significantly different from those of the LCT, NTTa, and HCC groups. Finally, we selected two of the 25 LC-specific genes and showed that these markers could be used to successfully discriminate among the different LC subtypes. Collectively, these novel results allow the identification of new genetic subgroups of LC and provide new candidate genes for use as early markers for active cirrhosis and HCC.

Biomarkers, Tumor↗
PubMed2004

Differential gene expression of Eph receptors and ephrins in benign human tissues and cancers.

BACKGROUND: Eph receptors and their ligands, the ephrins, represent a large class of cell-cell communication molecules with well-defined developmental functions. Their role in healthy adult tissues and in human disease is still largely unknown, although diverse roles in carcinogenesis have been postulated. METHODS: We established a set of fluorescent PCR probes and primers for the definition of individual gene expression profiles of 12 different Eph receptors and 8 ephrins in 13 different healthy tissues. The mRNA expression profiles were studied in human lung, colorectal, kidney, liver, and brain cancers. RESULTS: The family of Eph receptors/ephrins was widely expressed in adult tissues with organ-site-specific patterns: EphB6 was highest in the thymus, compatible with an involvement in T-cell maturation. Brain and testis shared a unique pattern with EphA6, EphA8, and EphB1 being the most prominent. EphA7 had a high abundance in the kidney vasculature. Ephrin-A3 was up-regulated 26-fold in lung cancer, and EphB2 was up-regulated 9-fold in hepatocellular carcinoma. EphA8 was down-regulated in colon cancer, and EphA1/EphA8 was down-regulated in glioblastomas. CONCLUSION: Eph/Ephrin genes are widely expressed in all adult organs with certain organ-site-specific patterns. Because their function in adult tissues remains unknown, further analysis of their role in disease may disclose new insights beyond their well-defined meaning in development.

Adult↗
PubMed2006

Transcriptional profiling of Alzheimer blood mononuclear cells by microarray.

We evaluated pathomechanisms and systemic manifestations of Alzheimer disease (AD), an aging-related dementing neurodegenerative disorder, by expression profiling. Blood mononuclear cell (BMC) transcriptomes of sporadic AD subjects and aged-matched normal elderly controls (NEC) were compared using the human NIA microarray. Relative to the NEC samples, the Alzheimer BMC exhibited a significant decline in the expression of genes concerned with cytoskeletal maintenance, cellular trafficking, cellular stress response, redox homeostasis, transcription and DNA repair. We observed decreased expression of several genes which may impact amyloid-beta production and the processing of the microtubule-associated protein tau. The microarray results were validated by quantitative real time PCR and revealed gender differences in the levels of altered gene expression. Our findings attest to the systemic nature of gene dys-regulation in sporadic AD, implicate disruption of cytoskeletal integrity, DNA repair mechanisms and cellular defenses in this condition, and suggest novel pathways of beta-amyloid deposition in this disease. BMC are highly accessible and may reflect molecular events germane to the neuropathophysiology of AD.

Aged↗
PubMed2001

Expression profile of genes coding for melanoma differentiation antigens and cancer/testis antigens in metastatic lesions of human cutaneous melanoma.

Vaccination-based therapy of melanoma has so far mainly focused on monovalent approaches using either melanoma differentiation antigens or cancer/testis antigens. To study the complementarity of expression from these two families of antigens recognized by T-cells, we screened 47 metastatic lesions of cutaneous melanoma for the expression of three melanoma differentiation antigens and eight cancer/testis antigens using reverse transcription-polymerase chain reaction (RT-PCR). The melanoma differentiation antigens were expressed in a somewhat higher percentage of lesions (94% positive for at least one marker) than the cancer/testis antigens (91% positive for at least one marker). Nearly all the melanoma metastases (98%) expressed at least one of the markers tested. One melanoma metastasis was negative for all the markers. Two out of 47 lesions did not express any of the three differentiation markers but expressed one or more of the cancer/testis antigens, indicating some additional potential for these antigens compared with the melanoma differentiation antigens. Therefore, we conclude that polyvalent immunotherapy using multiple epitopes from both families of antigens might increase the eligibility of melanoma patients and the efficacy of the treatment.

Antigens, Neoplasm↗
PubMed2006

Proteomic analysis of individual human embryos to identify novel biomarkers of development and viability.

OBJECTIVE: To develop a method to analyze the proteome of individual human blastocysts and identify differentially expressed proteins prior to implantation. DESIGN: Experimental study. SETTING: Research environment. PATIENT(S): Couples undergoing infertility treatment donated with consent cryopreserved human cleavage-stage embryos for research. INTERVENTION(S): Individual embryos were extracted and analyzed by time-of-flight mass spectrometry. MAIN OUTCOME MEASURE(S): The protein expression profiles of individual embryos. RESULT(S): Differential protein expression profiles were observed between early and expanded blastocysts, as well as between developing blastocysts and degenerate embryos. Significantly, several up-regulated and down-regulated proteins were detected in degenerating embryos. A search in the protein databases highlighted several candidates, including an inhibitor of Tcf-4 (transcription factor mediating Wnt signaling) and an apoptotic protease-activating factor. CONCLUSION(S): This is the first study to successfully analyze the proteome of individual human embryos. This study has shown that protein expression profiles relate to morphology, with degenerating embryos exhibiting significant up-regulation of several potential biomarkers that might be involved in apoptotic and growth-inhibiting pathways.

Biomarkers↗