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Results for “Biomarker Profiling”

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At least 1,063 records · Page 59Linked to original sources
PubMed2004

Androgen-independent prostate cancer is a heterogeneous group of diseases: lessons from a rapid autopsy program.

Understanding the biology of prostate cancer metastasis has been limited by the lack of tissue for study. We studied the clinical data, distribution of prostate cancer involvement, morphology, immunophenotypes, and gene expression from 30 rapid autopsies of men who died of hormone-refractory prostate cancer. A tissue microarray was constructed and quantitatively evaluated for expression of prostate-specific antigen, androgen receptor, chromogranin, synaptophysin, MIB-1, and alpha-methylacylCoA-racemase markers. Hierarchical clustering of 16 rapid autopsy tumor samples was performed to evaluate the cDNA expression pattern associated with the morphology. Comparisons were made between patients as well as within the same patient. Metastatic hormone-refractory prostate cancer has a heterogeneous morphology, immunophenotype, and genotype, demonstrating that "metastatic disease" is a group of diseases even within the same patient. An appreciation of this heterogeneity is critical to evaluating diagnostic and prognostic biomarkers as well as to designing therapeutic targets for advanced disease.

Aged↗
PubMed2006

Correlation of ErbB2 gene status, mRNA and protein expression in a panel of >100 human tumor xenografts of different origin.

INTRODUCTION: The receptor tyrosine kinase ErbB2 is an important prognostic marker and therapeutic target in breast cancer. The aim of this study was to investigate the correlation between ErbB2 gene amplification, mRNA and protein expression in a panel of >100 patient-derived nude mouse tumor xenografts of different histological origin. MATERIALS AND METHODS: Data were obtained using fluorescence in situ hybridization, GenChip expression analysis, immunohistochemistry and enzyme-linked immunosorbent assay (ELISA). Tumors included the following types: urinary bladder, breast, colon, stomach, kidney, liver, lung, melanoma, ovary, pancreas, prostate, uterus/cervix uteri and others. RESULTS: All tumors with high-level ErbB2 gene amplification expressed ErbB2 mRNA at a level >10-fold above average and protein at a level >20-fold above average (ELISA). Correlation was found between ErbB2 mRNA and protein expression. CONCLUSION: Based on expression data, cervical, gastric and adenocarcinomas of the lung emerged as new potential indications for ErbB2-directed cancer therapies.

Biomarkers, Tumor↗
PubMedDate not supplied

Beyond the suspicious thyroid fine needle aspirate. A review.

Fine needle aspiration (FNA) is currently the best diagnostic tool for thyroid nodules. However, the cytologic category of indeterminate or suspicious lesion, which is found in 10-15% of cases, remains a challenge. Since neither clinical presentation nor intraoperative frozen section is often helpful in differentiating these lesions and since surgical procedures for benign and malignant lesions differ, there is a clear need to develop ancillary tests. In this review we identify 12 potential markers of thyroid malignancy that have been examined in thyroid cytologic samples. Although many of these markers hold promise as adjuncts to FNA cytology, multicenter studies have often shown limitations in the predictive value of these assays due to lack of specificity, sensitivity or both. The recent development, however, of tissue microarray techniques to validate promising new markers suggests that improvements in the approach to indeterminate thyroid FNA samples may soon be at hand. This review presents a summary of the issues facing the development of a clinically useful diagnostic test in the differential diagnosis of thyroid nodules.

Biomarkers, Tumor↗
PubMed2026

Association of galectin-3 in systemic lupus erythematosus: A systematic review and meta-analysis.

BackgroundSystemic lupus erythematosus (SLE) is an autoimmune condition showing persistent profiling of inflammation and damage of organs and immune system. Amongst many biomarkers for such autoimmune diseases, Galectin-3 (Gal-3) a &#x3b2;-galactoside-binding lectin responsible for regulation, inflammation, and fibrosis of immune repsonses, has engrossed researchers for further investigations as a potential biomarker. However, correlation has been studied between circulating Galectin-3 levels and SLE but outcomes still remain inconsistent. Therefore, this systematic review and meta-analysis evaluated the association between circulating galectin-3 levels and SLE.Materials and MethodsPubMed, Scopus, ScienceDirect, Web of Science, and Embase databases are extensively used for literature search. The last database search was conducted on September 6, 2025. Eligible studies included case control studies reporting circulating galectin-3 levels in individuals with SLE and healthy controls. Two independent reviewers performed study selection and data extraction. Study quality was evaluated using the Newcastle-Ottawa Scale. Comprehensive Meta-Analysis software was used for statistical analysis. Pooled effect sizes were calculated as mean differences with 95% confidence intervals. Heterogeneity was assessed using the Cochrane Q test and I2 statistics, and publication bias was evaluated using Begg's funnel plot and Egger's regression analysis.ResultsSeven eligible studies were included in the meta-analysis. The pooled results showed that patients with SLE had significantly higher circulating Galectin-3 levels than healthy controls (mean difference = 8.48; 95% CI: 3.84-13.12; p < 0.0001). Substantial heterogeneity was observed across studies (Tau square: 32.57, Q = 196.03; p < 0.0001, I2 = 96.93%). Sensitivity analysis confirmed the stability of the overall findings. Begg's funnel plot and Egger's regression analysis indicated no publication bias among studies. Subgroup analysis supports the results of the overall analysis.ConclusionThis meta-analysis depicts that galectin-3 may serve as a biomarker associated with SLE pathogenesis and inflammatory activity due to significantly elevated levels of circulating galectin-3 levels in patients with systemic lupus erythematosus.

Humans↗
PubMed2002

Hodgkin and Reed-Sternberg cell-associated autoantigen CLIP-170/restin is a marker for dendritic cells and is involved in the trafficking of macropinosomes to the cytoskeleton, supporting a function-based concept of Hodgkin and Reed-Sternberg cells.

Little is known about the distribution in normal cells of CLIP-170, a linkage mediator between endocytic vesicles and microtubules, and restin, a splice variant encoded by the same gene and marker for Hodgkin and Reed-Sternberg (HRS) cells of Hodgkin disease. Although only trace amounts of CLIP-170/restin are present in peripheral blood mononuclear cell subpopulations, monocyte-derived dendritic cells (DCs) and interleukin-4 (IL-4) + CD40L-activated B cells express high levels of CLIP-170/restin. CLIP-170/restin colocalizes preferentially with membranes of intermediate macropinocytic vesicles, suggesting a new function of CLIP-170/restin in the trafficking of macropinosomes to the cytoskeleton, which is a crucial step in antigen presentation. The strong expression of CLIP-170/restin in HRS cells, DCs, and activated B cells underscores their functional similarities supporting a function-based concept of HRS cells as professional antigen-presenting cells.

Antigen-Presenting Cells↗
PubMed2004

Sample size for detecting differentially expressed genes in microarray experiments.

BACKGROUND: Microarray experiments are often performed with a small number of biological replicates, resulting in low statistical power for detecting differentially expressed genes and concomitant high false positive rates. While increasing sample size can increase statistical power and decrease error rates, with too many samples, valuable resources are not used efficiently. The issue of how many replicates are required in a typical experimental system needs to be addressed. Of particular interest is the difference in required sample sizes for similar experiments in inbred vs. outbred populations (e.g. mouse and rat vs. human). RESULTS: We hypothesize that if all other factors (assay protocol, microarray platform, data pre-processing) were equal, fewer individuals would be needed for the same statistical power using inbred animals as opposed to unrelated human subjects, as genetic effects on gene expression will be removed in the inbred populations. We apply the same normalization algorithm and estimate the variance of gene expression for a variety of cDNA data sets (humans, inbred mice and rats) comparing two conditions. Using one sample, paired sample or two independent sample t-tests, we calculate the sample sizes required to detect a 1.5-, 2-, and 4-fold changes in expression level as a function of false positive rate, power and percentage of genes that have a standard deviation below a given percentile. CONCLUSIONS: Factors that affect power and sample size calculations include variability of the population, the desired detectable differences, the power to detect the differences, and an acceptable error rate. In addition, experimental design, technical variability and data pre-processing play a role in the power of the statistical tests in microarrays. We show that the number of samples required for detecting a 2-fold change with 90% probability and a p-value of 0.01 in humans is much larger than the number of samples commonly used in present day studies, and that far fewer individuals are needed for the same statistical power when using inbred animals rather than unrelated human subjects.

Animals↗
PubMed2004

Bioinformatics strategies for translating genome-wide expression analyses into clinically useful cancer markers.

The DNA microarray has revolutionized cancer research. Now, scientists can obtain a genome-wide perspective of cancer gene expression. One potential application of this technology is the discovery of novel cancer biomarkers for more accurate diagnosis and prognosis, and potentially for the earlier detection of disease or the monitoring of treatment effectiveness. Because microarray experiments generate a tremendous amount of data and because the number of laboratories generating microarray data is rapidly growing, new bioinformatics strategies that promote the maximum utilization of such data are necessary. Here, we describe a method to validate multiple microarray data sets, a Web-based cancer microarray database for biomarker discovery, and methods for integrating gene ontology annotations with microarray data to improve candidate biomarker selection.

Biomarkers, Tumor↗
PubMed2006

Prognostic biomarkers in diffuse large B-cell lymphoma.

Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin's lymphoma. Although it represents a curable disease, less than half of the patients are cured with conventional chemotherapy. The highly variable outcome reflects a heterogeneous group of tumors, with different genetic abnormalities and response to therapy. The International Prognostic Index (IPI) is useful in predicting the outcome of DLBCL patients. However, patients with identical IPI still exhibit marked variability in survival, suggesting the presence of significant residual heterogeneity within each IPI category. The discovery of specific genetic alterations and the assessment of protein expression led to the identification of multiple novel single molecular markers capable of predicting the outcome of DLBCL patients independently of clinical variables. The recent application of DNA microarrays and tissue array technologies allowed a better understanding of the biology of lymphoma and the development of novel diagnostic tools capable of improving the current models for outcome prediction. However, much confusion exists in the literature regarding the importance of different prognostic biomarkers and their applicability in routine practice. This review summarizes the recent advances in our understanding of prognostic biomarkers in DLBCL and discusses whether this is the right time for biomarkers-guided risk-adjusted therapy.

Biomarkers, Tumor↗
PubMed2006

New developments in the detection of the clinical behavior of pheochromocytomas and paragangliomas.

Pheochromocytomas (PCC) are catecholamine-producing tumors that are, by definition, located in the adrenal medulla. Extra-adrenal catecholamine-producing tumors are called paragangliomas (PGL), which should be distinguished from head and neck paragangliomas, which are of parasympathetic origin. As is true for many (neuro)endocrine tumors, but unlike most other epithelial tumors, histopathological analysis does not allow a distinction to be made between PCC and PGL that will follow a benign course and those that have metastasized or will do so, a condition associated with poor prognosis. Therefore, many studies have been undertaken in the past decade, with the aim of providing a marker or a set of markers that allows clinical behavior in PCC and PGL to be predicted. Despite promising results in some areas, such as histopathological scoring systems, the use of the MIB-1 labeling index, and the analysis of telomerase activity, no single test or combination of tests has thus far yielded sufficiently high sensitivity and specificity to result in widespread acceptance in every day clinical practice. The relative rarity of PCC and PGL combined with a frequency of malignancy from as low as 2% up to 25% has hampered the power of past research and can only be overcome by multicenter collaborative efforts. In this article, recent attempts at marker detection, such as those mentioned above, as well as emerging knowledge on the molecular abnormalities in benign and malignant PCC and PGL will be presented.

Adrenal Gland Neoplasms↗
PubMed2004

Application of proteomic technologies to tumor analysis.

The sequencing of the human genome has had an enormous impact on the proteomic analysis of cancer by providing a sequence-based framework for understanding the human proteome of tumor cells, tissues, and biological fluids. There is intense interest in applying proteomic technologies to uncover, at the protein level, processes involved in neoplastic transformation and new biomarkers that correlate with early diagnosis, as well as to accelerate the development of new therapeutic targets. To that effect, new technologies are being developed in order to meet the needs for the high throughput and high sensitivity that is required for cancer-related applications of proteomics. These innovative technologies have greatly enhanced our ability to separate and characterize complex protein mixtures, and have aided our ability to identify proteins with greater sensitivity, thereby providing the groundwork for future scientific breakthroughs and possibly providing impetus for the development of personalized cancer therapy.

Animals↗
PubMed2006

Molecular classification of breast cancer: limitations and potential.

Reverse transcription polymerase chain reaction and DNA microarrays are increasingly used in the clinic and in clinical research as prognostic or predictive tests. Results from these tests led to novel risk stratification methods and to new molecular classification of breast cancer. Some of these tools already complement existing diagnostic tests and can aid medical decision making in some situations. Better understanding of the molecular classes of breast cancer, independent of their prognostic and predictive values, may also lead to new biological insights and eventually to better therapies that are directed toward particular molecular subsets. However, there is substantially less experience with these emerging technologies than with the more established methods, the accuracy of which is often overestimated. This review discusses some of the limitations and strengths of current gene expression-based molecular classification of breast cancer. To provide context for this discussion, we also briefly examine the performance of estrogen receptor immunohistochemistry, which represents an essential part of the routine diagnostic workup for all breast cancer patients.

Biomarkers, Tumor↗
PubMed2007

Recent advances in high-throughput molecular marker identification for superficial and invasive bladder cancers.

Bladder cancer is the fifth most common neoplasm in industrialized countries. Due to frequent recurrences of the superficial form of this disease, bladder cancer ranks as one of the most common cancers. Despite the description of a large number of tumor markers for bladder cancers, none have individually contributed to the management of the disease. However, the development of high-throughput techniques for simultaneous assessment of a large number of markers has allowed classification of tumors into clinically relevant molecular subgroups beyond those possible by pathological classification. Here, we review the recent advances in high-throughput molecular marker identification for superficial and invasive bladder cancers.

Biomarkers, Tumor↗
PubMed2007

IL-22 participates in an innate anti-HIV-1 host-resistance network through acute-phase protein induction.

Certain individuals are resistant to HIV-1 infection, despite repeated exposure to the virus. Although protection against HIV-1 infection in a small proportion of Caucasian individuals is associated with mutant alleles of the CCR5 HIV-1 coreceptor, the molecular mechanism underlying resistance in repeatedly HIV-1-exposed, uninfected individuals (EU) is unclear. In this study, we performed complementary transcriptome and proteome analyses on peripheral blood T cells, and plasma or serum from EU, their HIV-1-infected sexual partners, and healthy controls, all expressing wild-type CCR5. We report that activated T cells from EU overproduce several proteins involved in the innate immunity response, principally those including high levels of peroxiredoxin II, a NK-enhancing factor possessing strong anti-HIV activity, and IL-22, a cytokine involved in the production of acute-phase proteins such as the acute-phase serum amyloid A (A-SAA). Cell supernatants and serum levels of these proteins were up-regulated in EU. Moreover, a specific biomarker for EU detected in plasma was identified as an 8.6-kDa A-SAA cleavage product. Incubation of in vitro-generated myeloid immature dendritic cells with A-SAA resulted in CCR5 phosphorylation, down-regulation of CCR5 expression, and strongly decreased susceptibility of these cells to in vitro infection with a primary HIV-1 isolate. Taken together, these results suggest new correlates of EU protection and identify a cascade involving IL-22 and the acute phase protein pathway that is associated with innate host resistance to HIV infection.

Acute-Phase Proteins↗
PubMed2006

Comprehensive analysis of the expression of the metastasis-associated gene 1 in human neoplastic tissue.

CONTEXT: The metastasis-associated gene 1 (MTA1) is overexpressed in several human cancers. Recent reports suggest that MTA1 may play a role in cancer progression either through transcription repression and/or hormone receptor interactions. OBJECTIVE: To analyze MTA1 expression levels in a wide variety of human tumors. DESIGN: We used Oncomine, an Internet-based compendium of expression array data, to query more than 90 expression array studies, and we evaluated tissue microarrays composed of more than 3200 samples representing 138 different localized neoplasms. RESULTS: Both analyses show that MTA1 is ubiquitously expressed in benign and malignant tumors. The highest levels of MTA1 expression were observed in diffuse B-cell lymphoma (mean staining intensity, 3.9/4), basal cell carcinomas (3.7/4), and consistently in tumors of neuroendocrine descent such as paraganglioma (3.7/4) and carcinoid tumor (3.1/4). CONCLUSIONS: This study characterizes MTA1 expression for the first time across a broad spectrum of primary tumors, demonstrating expression in both benign and malignant neoplasms in addition to showing an association with neuroendocrine differentiation. We also found evidence that MTA1 expression is associated with tissue invasion but may not be sufficient for the progression to metastatic stages.

Biomarkers, Tumor↗